version .0 2fwrehu 20 software tools for - jay ponder lab

Version 8.4 February 2018

TINKERSoftware Tools for Molecular Design

TINKER

Software Tools for Molecular Design

Version 8.4

February 2018

Copyright © 1990-2018 by Jay William Ponder All Rights Reserved

2 TINKER User's Guide 2

Copyright © 1990-2018 by Jay William Ponder All Rights Reserved User's Guide Cover Illustration by Jay Nelson Courtesy of Prof. R. T. Paine, Univ. of New Mexico TINKER IS PROVIDED "AS IS" AND WITHOUT ANY WARRANTY EXPRESS OR IMPLIED. THE USER ASSUMES ALL RISKS OF USING THIS SOFTWARE. THERE IS NO CLAIM OF THE MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. YOU MAY MAKE COPIES OF TINKER FOR YOUR OWN USE, AND MODIFY THOSE COPIES. YOU MAY NOT DISTRIBUTE ANY MODIFIED SOURCE CODE OR DOCUMENTATION TO USERS AT ANY SITE OTHER THAN YOUR OWN. PLEASE SIGN AND RETURN THE TINKER LICENSE AGREEMENT IF YOU MAKE USE OF THIS SOFTWARE. V8.4 02/18

3 TINKER User's Guide 3

TINKER

Software Tools for Molecular Design

Version 8.4 February 2018

Table of Contents Page 1. Introduction to the Software 5 2. Installation on your Computer 7 3. Types of Input & Output Files 10 4. Potential Energy Programs 13 5. Additional Utility Programs & Scripts 19 6. Special Features & Methods 23 7. Use of the Keyword Control File 29 8. Force Field Parameter Sets 61 9. Descriptions of Source Routines 69 10. Descriptions of Global Variables 139 11. Index of Function & Subroutine Calls 167 12. Test Cases & Examples 196 13. Benchmark Results 198 14. Collaborators & Acknowledgments 202 15. References & Suggested Reading 204

4 TINKERUser'sGuide 4


1. IntroductiontotheSoftware WhatistheTINKERSoftware?WelcometotheTINKERmolecularmodelingpackage!TINKERisdesignedtobeaneasilyusedandflexible systemof programs and routines formolecularmechanics anddynamics aswell as otherenergy-basedandstructuralmanipulationcalculations.Itisintendedtobemodularenoughtoenabledevelopment of new computational methods and efficient enough to meet most productioncalculationneeds.Ratherthanincorporatingallthefunctionalityinonemonolithicprogram,TINKERprovidesasetofrelativelysmallprogramsthatinteroperatetoperformcomplexcomputations.Newprogramscanbeeasilyaddedbymodelerswithonlylimitedprogrammingexperience.FeaturesandCapabilitiesTheseriesofmajorprogramsincludedinthedistributionsystemperformthefollowingcoretasks: (1) buildingproteinandnucleicacidmodelsfromsequence (2) energyminimizationandstructuraloptimization (3) analysisofenergydistributionwithinastructure (4) moleculardynamicsandstochasticdynamics (5) simulatedannealingwithachoiceofcoolingschedules (6) normalmodesandvibrationalfrequencies (7) conformationalsearchandglobaloptimization (8) transitionstatelocationandconformationalpathways (9) fittingofenergyparameterstocrystaldata (10) distancegeometrywithpairwisemetrization (11) molecularvolumesandsurfaceareas (12) freeenergychangesforstructuralmutations (13) advancedalgorithmsbasedonpotentialsmoothing Manyofthevariousenergyminimizationandmoleculardynamicscomputationscanbeperformedonfullorpartialstructures,overCartesian,internalorrigidbodycoordinates,andincludingavarietyofboundaryconditionsandcrystalcelltypes.Otherprogramsareavailabletogeneratetimingdataandallowcheckingofpotentialfunctionderivativesforcodingerrors.Specialfeaturesareavailabletofacilitateinputandoutputofproteinandnucleicacidstructures.However,thebasiccoreroutineshavenoknowledgeofbiopolymerstructureandcanbeusedforgeneralmolecularsystems. Due to its emphasis on ease ofmodification, TINKER differs frommany other currently availablemolecularmodelingpackagesinthattheuserisexpectedtobewillingtowritesimple``front-end''programsandmakesomealterationsatthesourcecodelevel.Themainprogramsprovidedshouldbe consideredas templates for the users to changeaccording to theirwishes. All subroutines areinternallydocumentedandstructuredprogrammingpracticesareadheredtothroughout.Theresult,itishoped,willbeacalculationalsystemwhichcanbetailoredtolocalneedsanddesires. The coreTINKER systemconsists of nearly 135,000 lines of sourcewrittenentirely in a portableFortran77 superset. Use ismade of only some verycommon extensions that aid inwriting highlystructuredcode.Thecurrentversionofthepackagehasbeenportedtoawiderangeofcomputerswithnoorextremelyminimalchanges.Testedsystemsinclude:RedHatLinux,MicrosoftWindows9X/NT/2000/XP, Apple OS9 and OSX, HP/Compaq/DEC Alphas under Tru64 Unix and OpenVMS,Hewlett-Packard,IBM,SiliconGraphicsandSunworkstationsundereachvendor'sUnix.Atpresent,our new code iswritten on various Linux platforms, and occasionally tested for compatibility on


variousoftheothermachineandOScombinationslistedabove.Atpresent,weareintheprocessofconverting our primary development efforts fromFortran77 to amoremodern Fortrandialect. Amachine-translatedC version ofTINKER is currently available,and a hand-translated optimizedCversion of a previousTINKER release isavailable for inspection.Conversion to C or C++ is underconsideration,butnotbeingactivelypursuedatthistime. ThebasicdesignoftheenergyfunctionengineusedbytheTINKERsystemallowsusageofseveraldifferentparametersets.AtpresentwearedistributingparametersthatimplementAMBERff94andff96,CHARMM19and27,MM2,MM3,OPLS-UA,OPLS-AA,LiamDang'spolarizablepotentials,andourownAMOEBA(AtomicMultipoleOptimizedEnergeticsforBiomolecularApplications)parameters.Inmost cases, the sourcecode separates thegeometricmanipulations needed forenergy derivativesfromtheactualformoftheenergyfunctionitself.Severalotherliteratureparametersetsarebeingconsidered for possible future development (ENCAD,MMFF-94,MM4,UFF,etc.), andmany of thealternativepotential functionformsreportedintheliteraturecanbeimplementeddirectlyorafterminorcodechanges. Much of the software in the TINKER package has been heavily used and well tested, but somemodules are still in a fairly early stage of development. Further work on the TINKER system isplanned in threemain areas: (1) extension and improvement of the potential energy parametersincludingadditionalparameterizationandtestingofourpolarizablemultipoleAMOEBAforcefield,(2) coding of new computational algorithms including additional methods for free energydetermination,torsionalMonteCarloandmoleculardynamicssampling,advancedmethodsforlongrangeinteractions,bettertransitionstatelocation,andfurtherapplicationofthepotentialsmoothingparadigm, and (3) further development ofForceFieldExplorer, a Java-basedGUI front-end to theTINKERprogramsthatprovidesforcalculationsetup,launchandcontrolaswellasbasicmolecularvisualization.ContactInformation Questions and comments regarding theTINKERpackage, including suggestions for improvementsandchangesshouldbemadetotheauthor: ProfessorJayWilliamPonder DepartmentofChemistry,Box1134 WashingtonUniversityinSaintLouis OneBrookingsHall SaintLouis,MO63130U.S.A. office: LoudermanHall,Room453 phone: (314)935-4275 fax: (314)935-4481 email: [email protected] Inaddition,anInternetwebsitecontaininganonlineversionofthisUser'sGuide,themostrecentdistribution version of the full TINKER package and other useful information can be found athttp://dasher.wustl.edu/tinker, the Home Page for the TINKER Molecular ModelingPackage.


2. InstallationonyourComputer How to Obtain a Copy of TINKER The TINKER package is distributed on the Internet via either theweb site or the anonymous ftpaccountondasher.wustl.eduwithanIPnumberof128.252.208.48.Thisnodeisawebandfileserver located in the Ponder lab at Washington University School of Medicine. The package isavailable via the web and standard browsers from the TINKER home page athttp://dasher.wustl.edu/tinker/. Alternatively TINKER can be downloaded by loggingintodasher.wustl.edu via anonymous ftp (Username:anonymous, Password: "your email address")anddownloadingthesoftwarefromthe/pub/tinkersubdirectory.ThecompleteTINKERdistributionsaswellasindividualfilescanbedownloadedfromthissite. TheeasiestwaytogetTINKERrunningonyourmachineistousetheself-extractinginstallationkitforeitherLinux,Windows,orMacintoshOSX10.3.The installerwillguideyou throughcompletesetup of TINKER and the Force Field Explorer (FFE) GUI, and perform all required configurationchores. The installer kits for the three supported systems are tinker4.2-linux.sh,tinker4.2-windows.exe and tinker4.2-macosx.sit. The Linux and Windows kits eachcontain a private copy of a Java and Java3D run-time environment for usewith the package. TheMacintosh version requires an OS X 10.3 (Panther) system for installation. The native Javaimplementation is used on Macs, and the Java3D package must be downloaded from Apple andinstalledpriortousingTINKERwithForceFieldExplorer.PrebuiltTINKERExecutables TheTINKERpackageisalsoavailableascompressedUnixtararchives,Windowszipfiles,andasacomplete set of uncompressed source and data files. Binaries are provided formachines runningWindows9X/ME/NT/2000/XP,Linux,andAppleMacOSX.Allof theseexecutablesarepresent instandard compressed formats as individual programs or as complete sets of executables. It isexpected that other Unix users and PC users who need specially customized versions, will buildbinaries for their specific system. Sites with access to the Unix tar, compress and uncompresscommands should simply obtain the archive filetinker.tar.Z. Alternatively,tinker.tar.gzand tinker.zip containing identical distributions compressed to GNU gzip and Windows ZIPformatarealsoprovided.Ifyouchoosetodownloadindividualfiles,youwillneedataminimumthecontents of the /doc, /source and /params subdirectories. Also required are the compile/buildscripts from the subdirectory named for your machine type. Other areas contain test cases andexamples,benchmarkresults,machine-translatedCcode,andtheForceFieldExplorerJavaGUIforTINKER.TheentireTINKERpackage,afterbuilding theexecutables,will require fromabout40 toover 150megabytes of disk space depending on the components installed and the use of sharedlibrariesintheexecutables. Building your Own Executables The compilation andbuilding of theTINKER executables should be easy formost of the commonworkstationandPCclasscomputers.Weprovideinthe/makeareaaUnix-styleMakefilethatwithsomemodificationcanbeusedtobuildTINKERonmostUnixmachines.AsasimpleralternativetoMakefiles for the Unix versions,we also providemachine-specific directorieswith three separateshellscriptstocompilethesource,buildanobjectlibrary,andlinkbinaryexecutables.Threesimilarcommand filesareprovidedforWindows,MacintoshandOpenVMSsystems.CompilationonUnixworkstationsshouldusethevendorsuppliedFortrancompiler,ifavailable.ThepublicdomainGNU


g77Fortrancompileravailablefromhttp://gcc.gnu.org/ isalsocapableofbuildingTINKERonLinuxandotherUnix-basedmachines.TheLinuxexecutablesweprovidearebuiltwiththeIntelFortranforLinux8.0compiler.ThePortlandGroup(PGI)andAbsoftProFortrancompilershavealsobeen tested under Linux, both ofwhich generate executables roughly comparable in speed to theIntelcompiler.OnLinux,theg77executablestendtoexhibitdegradedperformancecomparedwithexecutablesfromcommercialcompilers.Somebenchmarkresultsareprovidedina latersectionofthisUser'sGuideFortheMacintoshwedistributeexecutablesbuiltunderAppleOSX10.3withtheGNUg77compiler.TINKERalsobuildsontheMacintoshusingtheAbsoftProFortrancompiler.ForPCsrunningWindows9X/NT/2000/XP,thedistributedTINKERexecutablesarebuiltundertheIntelFortranforWindows8.0compiler.AlternativeWindowscompilerssuchasCompaqVisualFortran,Lahey/FujitsuandThePortlandGroupcompilers,andGNUg77underCygwinhavebeentestedandshowntobuildTINKERcorrectly.PleaseseetheREADMEfilesineachofthemachine-specificareasforfurtherinformation. The first step in building TINKER using the script files is to run the appropriatecompile.make script for your operating system and compiler version. Next you must use alibrary.makescripttocreateanarchiveofobjectcodemodules.Finally,runalink.makescripttoproducethecompletesetofTINKERexecutables.Theexecutablescanberenamedandmovedtowhereveryoulikebyeditingandrunningthe``rename''script.Thesestepswillproduceexecutablesthatcanrunfromthecommandline,butwithoutthecapabilitytointeractwiththeFFEGUI.BuildingFFE-enabledTINKERexecutablesinvolvesreplacingthesockets.fsourcefilewithsockets.c,andincludedtheobjectfromtheCcodeintheTINKERobject library.Thenexecutablesmustbelinkedagainst Java libraries in addition to the usual resources. Sample compgui.make andlinkgui.makescriptsareprovidedforsystemscapableofbuildingGUI-enabledexecutables. Regardless of your target machine, only a few small pieces of code can possibly requireattentionpriortobuilding.Thefirsttwoarethesystemdependenttimeanddateroutinesfoundinclock.fandcalendar.frespectively.Nextistheopenend.froutinethatfacilitatesappendingdatatotheendofanexistingdiskfile.Pleaseuncommentthesectionsoftheseroutinesneededforyourcomputertype.Versionofthesesystemdependentroutinessuitableforeachsystemarealsoprovidedinthedirectoryforeachmachine/OStype.Thefinalsetofpossiblesourcealterationsaretothe master array dimensions found in the include file sizes.i. The most basic limit is on thenumber of atoms allowed, ``maxatm''. This parameter can be set to 10000 or more on mostworkstations. Personal computers with minimal memory may need a lower limit, perhaps 1000atoms,dependingonavailablememory,swapspaceandotherresources.Adescriptionoftheotherparametervaluesiscontainedintheheaderofthefile.Notethatinordertokeepthecodecompletelytransparent, TINKER does not implement any sort of dynamic memory allocation or heap datastructure. This requires thatsizes.i dimensioning values be set at least as largeas the biggestproblem you intend to run. Obviously, you should not set the array sizes to unnecessarily largevalues, since this can tax your compute resources andmay result in performance degradation orovertfailureoftheexecutables.DocumentationandOtherInformation The documentation for the TINKER programs, including the guide you are currently reading, islocatedinthe/pub/tinker/docsubdirectory.ThedocumentationwaspreparedusingtheApplixwareWordsandGraphicsprograms.Portableversionsofthedocumentationareprovidedasasciitextin.txt files and in Adobe Acrobat .pdf file formats. Please read and return by mail the TINKERlicense. In particular, we note that TINKER is not ``Open Source'' as users are prohibited fromredistribution of original ormodifiedTINKER source code or binaries to other parties.While ourintentistodistributetheTINKERcodetoanyonewhowantsit,thePonderLabwouldliketoremainthesoledistributionsiteandkeeptrackofresearchersusingthepackage.Thereturnedlicenseforms


also help us justify further development of TINKER.When newmodules and capabilities becomeavailable,andwhenthealmostinevitablebugsareuncovered,wewillattempttonotifythosewhohavereturnedalicenseform.Finally,weremindyouthatthissoftwareiscopyrighted,andaskthatitnotberedistributedinanyform. WheretoDirectQuestions Specific questions about the building or use of the TINKER package should be directed [email protected]. TINKER related questions or comments ofmore general interestcanbesenttotheComputationalChemistryList(http://www.ccl.net/)runbyJanLabanowskiattheUniversityofNotreDame.TheTINKERdevelopersmonitorthislistandwillrespondtothelistortheindividualposterasappropriate.


3. TypesofInput&OutputFiles ThissectiondescribesthebasicfiletypesusedbytheTINKERpackage.Let'ssayyouwishtoperformacalculationonaparticularsmallorganicmolecule.Assumethatthefilenamechosenforourinputandoutputfilesissample.ThenalloftheTINKERfileswillresideonthecomputerunderthenamesample.xxxwhere.xxxisanyoftheseveralextensiontypestobedescribedbelow. SAMPLE.XYZ The.xyzfileisthebasicTINKERCartesiancoordinatesfiletype.Itcontainsatitlelinefollowedbyone line for each atom in the structure. Each line contains: the sequential number within thestructure,anatomicsymbolorname,X-,Y-,andZ-coordinates,theforcefieldatomtypenumberoftheatom,anda listof theatomsconnected to thecurrentatom.Except forprogramswhosebasicoperation is in torsional space, all TINKER calculations are done from some version of the.xyzformat. SAMPLE.INT The.intfilecontainsaninternalcoordinatesrepresentationofthemolecularstructure.Itconsistsofatitle linefollowedbyonelineforeachatominthestructure.Eachlinecontains:thesequentialnumberwithin the structure, anatomic symbol or name, the force field atom type number of theatom,andinternalcoordinatesintheusualZ-matrixformat.Foreachatomtheinternalcoordinatesconsistofadistancetosomepreviouslydefinedatom,andeithertwobondanglesorabondangleand a dihedral angle to previousatoms. The length,angleanddihedral definitions do not have torepresent real bonded interactions.Following the lastatomdefinition are two optional blank lineseparatedsetsofatomnumberpairs.Thefirstlistcontainspairsofatomsthatarecovalentlybonded,butwhosebondlengthwasnotusedaspartoftheatomdefinitions.Thesepairsaretypicallyusedtocloseringstructures.Thesecondlistcontains``bonds''thataretobebroken,i.e.,pairsofatomsthatarenotcovalentlybonded,butwhichwereusedtodefineadistanceintheatomdefinitions. SAMPLE.KEY Thekeywordparameterfilealwayshastheextension.keyandisoptionallypresentduringTINKERcalculations.Itcontainsvaluesforanyofawidevarietyofswitchesandparametersthatareusedtochangethecourseofthecomputationfromthedefault.Thedetailedcontentsofthisfileisexplainedin a latter section of this User's Guide. If a molecular system specific keyfile, in this casesample.key,isnotpresent,thetheTINKERprogramwilllookinthesamedirectoryforagenericfilenamedtinker.key. SAMPLE.DYN The.dynfilecontainsvaluesneededtorestartamolecularorstochasticdynamicscomputation.Itstoresthecurrentposition,currentvelocityandcurrentandpreviousaccelerationsforeachatom,aswellas thesizeandshapeofanyperiodicboxorcrystalunit cell.This informationcanbeused tostartanewdynamicsrunfromthefinalstateofapreviousrun.Uponstartup,thedynamicsprogramsalwayscheckforthepresenceofa.dynfileandmakeuseofitwheneverpossible.The.dynfileisupdatedconcurrentwiththesavingofanewdynamicstrajectorysnapshot. SAMPLE.END


The .end file type provides a mechanism to gracefully stop a running TINKER calculation. Atappropriatecheckpointsduringacalculation,TINKERwill testfor thepresenceofasample.endfile, and if found will terminate the calculation after updating the output. The .end file can becreatedatanytimeduringacomputation,andwillbedetectedwhenthenextcheckpointisreached.Thefilemaybeofzerosize,anditscontentsareunimportant.InthecurrentversionofTINKER,the.endmechanismisonlyavailablewithindynamics-basedprograms. SAMPLE.001,SAMPLE.002,.... Several types of computations produce files containing a three ormore digit extension (.001 asshown;or.002,.137,.5678,etc.).Thesearereferredtoascyclefiles,andareusedtostorevarioustypesofoutputstructures.Thecyclefilesfromagivencomputationareidenticalininternalstructuretoeitherthe.xyzor.intfilesdescribedabove.Forexample,thevibrationalanalysisprogramcansavethetenthnormalmodeinsample.010.Amoleculardynamics-basedprogrammightsaveitstenth0.1picosecondframe(oranenergyminimizeritstenthpartiallyminimizedintermediate)inafileofthesamename. SAMPLE.LOG TheForceFieldExplorerinterfacetoTINKERsavesresultsofallcalculationslaunchedfromtheGUIto a log filewith the.log suffix. Any output thatwould normally be directed to the screenafterstartingaprogramfromthecommandlineisappendedtothislogfilebyForceFieldExplorer. SAMPLE.ARC ATINKERarchive file is simplya seriesof.xyzCartesiancoordinate filesappended togetheroneafter another. This file can be used to condense the results from intermediate stages of anoptimization,framesfromamoleculardynamicstrajectory,orsetofnormalmodevibrationsintoasinglefileforstorage.TINKERarchivefilescanbedisplayedas``movies''bytheForceFieldExplorermodelingprogram. SAMPLE.PDB This file type contains coordinate information in the PDB format developed by the BrookhavenProteinDataBankfordepositionofmodelstructuresbasedonmacromolecularX-raydiffractionandNMR data. Although TINKER itself does not use .pdb files directly for input/output, auxiliaryprograms are provided with the system for interconverting .pdb files with the .xyz formatdescribedabove. SAMPLE.SEQ Thisfiletypecontainstheprimarysequenceofabiopolymerinthestandardone-lettercodewith50residues per line. The .seq file for a biopolymer is generated automatically when a PDB file isconverted toTINKER.xyz format orwhen using the PROTEIN or NUCLEIC programs to build astructure from sequence It is required for the reverse conversion of a TINKER file back to PDBformat.. SAMPLE.FRAC Thefractionalcoordinatescorrespondingtotheasymmetricunitofacrystalunitcellarestoredinthe.fracfile.Theinternalformatofthisfileisidenticaltothe.xyzfile;exceptthatthecoordinatesarefractionalinsteadofinAngstromunits.


SAMPLE.XMOL TheARCHIVEprogramhas theoptionofconvertingaseriesof.xyzcycle files intoanXMakemolXYZfile.ThesefilescanbedisplayedasamovieusingtheXMakemoldisplayprogram.Notethatthe.xmolfileformatdoesnotcontainTINKERatomtypeinformation,soitisnotpossibletoconvertan.xmolfilebackintoaTINKER.xyzfile. SAMPLE.CAR TheARCHIVEprogramhas the option of convertinga series of.xyz cycle files intoanAccelerysInsightIIcoordinatearchivefile.ThesefilescanbedisplayedasamovieusingtheInsightIIdisplayprogram.Notethatthe.carfileformatdoesnotcontainTINKERatomtypeinformation,soitisnotpossibletoconverta.carfilebackintoaTINKER.XYZfile. PARAMETERFILES ThepotentialenergyparameterfilesdistributedwiththeTINKERpackageallendintheextension.prm, although this is not required by the programs themselves. Each of these files contains adefinitionofthepotentialenergyfunctionalformsforthatforcefieldaswellasvaluesforindividualenergy parameters. For example, the mm3pro.prm file contains the energy parameters anddefinitionsneededforaprotein-specificversionoftheMM3forcefield.


4. PotentialEnergyPrograms This section of the manual contains a brief description of each of the TINKER potential energyprograms.Adetailedexampleshowinghowtoruneachprogramis includedina latersection.Theprograms listed beloware all part of themain, supported distribution. Additional sourcecode forvariousunsupportedprogramscanbefoundinthe/otherdirectoryoftheTINKERdistribution. ALCHEMY A simple program to perform very basic free energy perturbation calculations. This program isprovided mostly for demonstration purposes. For example, we use ALCHEMY in a molecularmodelingcourselaboratoryexercisetoperformsuchclassicmutationsaschloridetobromideandethanetomethanolinwater.Thepresentversionusestheperturbationformulaandwindowingwithanexplicitmappingofatomsinvolvedinthemutation(``AMBER''-style),insteadofthermodynamicintegrationandindependentfreelypropagatinggroupsofmutatedatoms(``CHARMM''-style).SomeofthecodespecifictothisprogramislimitedtotheAMBERandOPLSpotentialfunctionalforms,butcouldbeeasilygeneralizedtohandleotherpotentials.Amoregeneralandsophisticatedversioniscurrentlyunderdevelopment. ANALYZE Providesinformationabouta specificmolecular structure.Theprogramwill ask for thenameofastructure file, which must be in the TINKER .xyz file format, and the type of analysis desired.Optionsallowoutputof: (1) totalpotentialenergyof thesystem, (2)breakdownof theenergybypotentialfunctiontypeoroverindividualatoms,(3)computationofthetotaldipolemomentanditscomponents,momentsofinertiaandradiusofgyration,(4)listingoftheparametersusedtocomputeselectedinteractionenergies,(5)energiesassociatedwithspecifiedindividualinteractions. ANNEAL Performs a molecular dynamics simulated annealing computation. The program starts from aspecifiedinputmolecularstructureinTINKER.xyzformat.ThetrajectoryisupdatedusingeitheramodifiedBeemanoravelocityVerletintegrationmethod.Theannealingprotocolisimplementedbyallowing smooth changes between starting and final values of the system temperature via theGroningenmethodofcouplingtoanexternalbath.Thescalingcanbelinearorsigmoidalinnature.Inaddition, parameters such ascutoff distance can be transformed alongwith the temperature. Theusermustinputthedesirednumberofdynamicsstepsforboththeequilibrationandcoolingphases,atimeintervalforthedynamicssteps,andanintervalbetweencoordinate/trajectorysaves.Allsavedcoordinatesetsalongthetrajectoryareplacedinsequentiallynumberedcyclefiles. DYNAMIC Performsamoleculardynamics(MD)orstochasticdynamics(SD)computation.Startseitherfromaspecifiedinputmolecularstructure(an.xyzfile)orfromastructure-velocity-accelerationsetsavedfroma previous dynamics trajectory (a restart froma.dyn file).MD trajectories are propagatedusingeitheramodifiedBeemanoravelocityVerlet integrationmethod.SDisimplementedviaourownderivationofavelocityVerlet-basedalgorithm.Inadditiontheprogramcanperformfullcrystalcalculations,andcanoperateinconstantenergymodeorwithmaintenanceofadesiredtemperatureand/orpressureusingtheGroningenmethodofcouplingtoexternalbaths.Theusermustinputthedesirednumberofdynamicssteps,atimeintervalforthedynamicssteps,andanintervalbetweencoordinate/trajectory saves. Coordinate sets along the trajectory can be saved as sequentially


numberedcyclefilesordirectlytoaTINKERarchive.arcfile.Atthesametimethatapointalongthetrajectoryissaved,thecompleteinformationneededtorestartthetrajectoryfromthatpointisupdatedandstoredinthe.dynfile. GDA AprogramtoimplementStraub'sGaussianDensityAnnealingalgorithmoveraneffectiveseriesofanalytically smoothed potential energy surfaces. This method can be viewed as an extendedstochastic version of the diffusion equationmethod of Scheraga,et al., and also hasmany similarfeatures to the TINKER Potential Smoothing and Search (PSS) series of programs. The currentversionofGDAissimilartobutdoesnotexactlyreproduceStraub'spublishedmethodandislimitedto argon clusters and other simple systems involving only van der Waals interactions; furthermodificationanddevelopmentofthiscodeiscurrentlyunderwayinthePonderresearchgroup.Aswithotherprogramsinvolvingpotentialsmoothing,GDAcurrentlyrequiresuseofthesmooth.prmforcefieldparameters. MINIMIZE TheMINIMIZEprogramperformsalimitedmemoryL-BFGSminimizationofaninputstructureoverCartesian coordinates using a modified version of the algorithm of Jorge Nocedal. The methodrequires only the potential energy and gradient at each step along theminimization pathway. Itrequires storage space proportional to the number of atoms in the structure. The MINIMIZEprocedureisrecommendedforpreliminaryminimizationoftrialstructurestoanrmsgradientof1.0to 0.1 kcal/mole/≈. It hasa relatively fast cycle time and is tolerant of poor initial structures, butconverges ina slow, linear fashionnear theminimum.Theusersupplies thenameof theTINKER.xyz coordinates file and a target rms gradient value at which the minimization will terminate.Outputconsistsofminimizationstatisticswrittentothescreenorredirectedtoanoutputfile,andthenewcoordinateswrittentoupdated.xyzfilesortocyclefiles. MINIROT TheMINIROTprogramuses thesame limitedmemoryL-BFGSmethodasMINIMIZE,butperformsthecomputationintermsofdihedralanglesinsteadofCartesiancoordinates.Outputissavedinanupdated.intfileorincyclefiles. MINRIGID TheMINRIGIDprogramissimilartoMINIMIZEexceptthatitoperatesonrigidbodiesstartingfromaTINKER.xyzcoordinatefileandtherigidbodygroupdefinitionsfoundinthecorresponding.keyfile.Outputissavedinanupdated.xyzfileorincyclefiles. MONTE The MONTE program implements the Monte Carlo Minimization algorithm developed by HaroldScheraga'sgroupandothers.Theprocedure takesMonteCarlosteps foreithera singleatomorasingletorsionalangle,thenperformsaminimizationbeforeapplicationoftheMetropolissamplingmethod.This results ineffective sampling ofamodified potential surfacewhere the only possibleenergylevelsarethoseoflocalminimaontheoriginalsurface.Theprogramcanbeeasilymodifiedtoelaborateontheavailablemoveset. NEWTON


A truncatedNewtonminimizationmethodwhich requires potential energy, gradient and Hessianinformation.ThisprocedurehassignificantadvantagesoverstandardNewtonmethods,andisableto minimize very large structures completely. Several options are provided with respect tominimization method and preconditioning of the Newton equations. The default options arerecommendedunlesstheuserisfamiliarwiththemathinvolved.ThisprogramoperatesinCartesiancoordinatespaceandisfairlytolerantofpoorinputstructures.Typicalalgorithmiterationtimesarelongerthanwithnonlinearconjugategradientorvariablemetricmethods,butmanyfeweriterationsarerequiredforcompleteminimization.NEWTONisusuallythebestchoiceforminimizationstothe0.01 to 0.000001 kcal/mole/≈ level of rms gradient convergence. Tests for directions of negativecurvature can be removed, allowing NEWTON to be used for optimization to conformationaltransitionstatestructures(thisonlyworksifthestartingpointisveryclosetothetransitionstate).InputconsistsofaTINKER.xyzcoordinatesfile;outputisanupdatedsetofminimizedcoordinatesandminimizationstatistics. NEWTROT TheNEWTROTprogramissimilartoNEWTONexceptthatitrequiresa.intfileasinputandthenoperatesintermsofdihedralanglesastheminimizationvariables.SincethedihedralspaceHessianmatrixofanarbitrarystructureisoftenindefinite,thismethodwilloftennotperformaswellastheother,simplerdihedralanglebasedminimizers. OPTIMIZE TheOPTIMIZEprogramperformsaoptimallyconditionedvariablemetricminimizationofaninputstructureoverCartesiancoordinatesusinganalgorithmduetoWilliamDavidon.Themethoddoesnotperformlinesearches,butrequirescomputationofenergiesandgradientsaswellasstorageforanestimateof the inverseHessianmatrix.TheprogramoperatesonCartesiancoordinates fromaTINKER .xyz file. OPTIMIZE will typically converge somewhat faster and more completely thanMINIMIZE.However,theneedtostoreandmanipulateafullinverseHessianestimatelimitsitsusetostructures containing less than a few hundred atoms onworkstation classmachines. Aswith theother minimizers, OPTIMIZE needs input coordinates and an rms gradient cutoff criterion. Theoutputcoordinatesaresavedinupdated.xyzfilesorascyclefiles. OPTIROT TheOPTIROTprogram is similar toOPTIMIZE except that it operates on dihedral angles startingfromaTINKER.intinternalcoordinatefile.ThisprogramisusuallythepreferredmethodformostdihedralangleoptimizationproblemssinceTruncatedNewtonmethodsappear,inourhands,tolosesomeoftheirefficacyinmovingfromCartesiantotorsionalcoordinates. OPTRIGID TheOPTRIGIDprogramissimilartoOPTIMIZEexceptthatitoperatesonrigidbodiesstartingfromaTINKER.xyzcoordinatefileandtherigidbodyatomgroupdefinitionsfoundinthecorresponding.keyfile.Outputissavedinanupdated.xyzfileorincyclefiles. PATH AprogramthatimplementsavariantofElber'sLagrangianmultiplier-basedreactionpathfollowingalgorithm.Theprogramtakesas inputapairofstructuralminimaasTINKER.xyz files,andthengeneratesauserspecifiednumberofpointsalongapaththroughconformationalspaceconnectingthe inputstructures.The intermediatestructuresareoutputasTINKERcycle files, and thehigher


energyintermediatescanbeusedasinputtoaNewton-basedoptimizationtolocateconformationaltransitionstates. PSS Implementsourversionofapotentialsmoothingandsearchalgorithmfortheglobaloptimizationofmolecular conformation. An initial structure in .xyz format is first minimized in Cartesiancoordinates on a series of increasingly smoothed potential energy surfaces. Then the smoothingprocedureisreversedwithminimizationoneachsuccessivesurfacestartingfromthecoordinatesoftheminimumontheprevioussurface.Alocalsearchprocedureisusedduringthebacktrackingtoexploreforalternativeminimabetterthantheonefoundduringthecurrentminimization.Thefinalresult isusuallyaverylowenergyconformationor,infavorablecases,theglobalenergyminimumconformation.Theminimumenergycoordinatesetsfoundoneachsurfaceduringboththeforwardsmoothingandbacktrackingproceduresareplacedinsequentiallynumberedcyclefiles. PSSRIGID ThisprogramimplementsthepotentialsmoothingandsearchmethodasdescribedaboveforthePSSprogram,butperformsthecomputationintermsofkeyfile-definedrigidbodyatomgroupsinsteadofCartesiancoordinates.Outputissavedinnumberedcyclefileswiththe.xyzfileformat. PSSROT ThisprogramimplementsthepotentialsmoothingandsearchmethodasdescribedaboveforthePSSprogram,butperformsthecomputationintermsofasetofuser-specifieddihedralanglesinsteadofCartesiancoordinates.Outputissavedinnumberedcyclefileswiththe.intfileformat. SADDLE A program for the location of a conformational transition state between two potential energyminima. SADDLE uses a conglomeration of ideas from the Bell-Crighton quadratic path and theHalgren-Lipscombsynchronoustransitmethods.Thebasicideaistoperformanonlinearconjugategradient optimization in a subspace orthogonal to a suitably defined reaction coordinate. Theprogram requires as input the coordinates (TINKER .xyz files) of the two minima and an rmsgradient convergence criterion for the optimization. The current estimate of the transition statestructureiswrittentothefileTSTATE.XYZ.CrudetransitionstatestructuresgeneratedbySADDLEcan sometimes be refined using the NEWTON program. Optionally, a scan of the interconversionpathwaycanbemadeateachmajoriteration. SCAN A program for general conformational search of an entire potential energy surface via a basinhopping method. The program takes as input a TINKER .xyz coordinates file which is thenminimized to find the first local minimum for a search list. A series of activations along variousnormal modes from this initial minimum are used as seed points for additional minimizations.Wheneverapreviouslyunknown localminimum is located it isadded to thesearch list.Whenallminima on the search list have been subjected to the normal mode activation without locatingadditional newminima, the program terminates. The individual localminimaarewritten to cyclefilesastheyarediscovered.WhiletheSCANprogramcanbeusedonstandardundeformedpotentialenergy surfaces, we have found it to be most useful for quickly ``scanning'' a smoothed energysurfacetoenumeratethemajorbasinsofattractionspaningtheentiresurface.


SNIFFER A program that implements the Sniffer global optimization algorithm of Butler and Slaminka, adiscreteversionofGriewank'sglobalsearchtrajectorymethod.TheprogramtakesaninputTINKER.xyzcoordinatesfileandshakesitvigorouslyviaamodifieddynamicstrajectorybefore,hopefully,settling into a low lying minimum. Some trial and error is often required as the currentimplementation is sensitive tovariousparametersand tolerances thatgovern thecomputation.Atpresent,theseparametersarenotuseraccessible,andmustbealteredinthesourcecode.However,this method can do a good job of quickly optimizing conformation within a limited range ofconvergence. TESTGRAD TheTESTGRADprogramcomputesandcomparestheanalyticalandnumericalfirstderivatives(i.e.,thegradientvector)of thepotentialenergy foraCartesiancoordinateinput structure.Theoutputcanbeusedtotestordebugthecurrentpotentialoranyaddeduserdefinedenergyterms. TESTHESS The TESTHESS program computes and compares the analytical and numerical second derivatives(i.e., the Hessian matrix) of the potential energy for a Cartesian coordinate input structure. Theoutputcanbeusedtotestordebugthecurrentpotentialoranyaddeduserdefinedenergyterms. TESTLIGHT A program to compare the efficiency of different nonbonded neighbor methods for the currentmolecularsystem.TheprogramtimesthecomputationofenergyandgradientforthevanderWaalsandcharge-chargeelectrostaticpotentialtermsusingasimpledoubleloopoverallinteractionsandusingtheMethodofLightsalgorithmtoselectneighbors.TheresultscanbeusedtodecidewhethertheMethodofLightshasanyCPUtimeadvantageforthecurrentstructure.Bothmethodsshouldgiveexactlythesameanswerinallcases,sincetheidenticalindividualinteractionsarecomputedbybothmethods. The default double loopmethod is fasterwhen cutoffsare not used, orwhen the cutoffspherecontainsabouthalformoreofthetotalsystemofunitcell.Incaseswherethecutoffsphereismuch smaller than the system size, the Method of Lights can be much faster since it avoidsunnecessarycalculationofdistancesbeyondthecutoffrange. TESTROT TheTESTROTprogramcomputesandcompares theanalyticalandnumerical firstderivatives (i.e.,thegradientvector)ofthepotentialenergywithrespecttodihedralangles.InputisaTINKER.intinternalcoordinatefile.Theoutputcanbeusedtotestordebugthecurrentpotential functionsoranyaddeduserdefinedenergyterms. TIMER AsimpleprogramtoprovidetimingstatisticsforenergyfunctioncallswithintheTINKERpackage.TIMER requires an input.xyz file and outputs the CPU time (wall clock time on somemachinetypes)neededtoperformaspecifiednumberofenergy,gradientandHessianevaluations. TIMEROT


ThisprogramissimilartoTIMER,onlyitoperatesoverdihedralanglesviainputofaTINKER.intinternalcoordinatefile.Inthecurrentversion,thetorsionalHessianiscomputednumericallyfromtheanalyticaltorsionalgradient. VIBRATE Aprogramtoperformvibrationalanalysisbycomputinganddiagonalizing the fullHessianmatrix(i.e., the secondpartial derivatives) for an input structure (aTINKER.xyz file). Eigenvalues andeigenvectorsofthemassweightedHessian(i.e., thevibrationalfrequenciesandnormalmodes)arealsocalculated.Structurescorrespondingtoindividualnormalmodemotionscanbesavedincyclefiles. VIBROT The program VIBROT forms the torsional Hessian matrix via numerical differentiation of theanalyticaltorsionalgradient.TheHessianisthendiagonalizedandtheeigenvaluesareoutput.ThepresentversiondoesnotcomputethekineticenergymatrixelementsneededtoconverttheHessianintothetorsionalnormalmodes;thiswillbeaddedinalaterversion.TherequiredinputisaTINKER.intinternalcoordinatefile. XTALFIT TheXTALFITprogramisofuseintheautomatedfittingofpotentialparameterstocrystalstructureandthermodynamicdata.XTALFITtakesasinputseveralcrystalstructures(TINKER.xyzfileswithunitcellparametersincorrespondingkeyfiles)aswellasinformationonlatticeenergiesanddipolemomentsofmonomers.ThecurrentversionusesanonlinearleastsquaresoptimizationtofitvanderWaals and electrostatic parameters to the input data. Bounds can be placed on the values of theoptimizationparameters. XTALMIN A program to perform full crystal minimizations. The program takes as input the structurecoordinatesandunitcelllatticeparameters.ItthenalternatescyclesofNewton-styleoptimizationofthestructureandconjugategradientoptimizationofthecrystallatticeparameters.Thisalternatingminimization is slower thanmore direct optimization of all parameters at once, but is somewhatmorerobustinourhands.Thesymmetryoftheoriginalcrystalisnotenforced,sointerconversionofcrystalformsmaybeobservedinsomecases.


5. AdditionalUtilityPrograms&Scripts ThissectionofthemanualcontainsabriefdescriptionofeachoftheTINKERstructuremanipulation,geometriccalculationandauxiliaryprograms.Adetailedexampleshowinghowtoruneachprogramis included in a later section. The programs listed below are all part of the main, supporteddistribution.Additional sourcecode forvariousunsupportedprogramscanbe found in the/otherdirectoryoftheTINKERdistribution. ARCHIVE A program for concatenating TINKER cycle files into a single archive file; useful for storing theintermediate results of minimizations, dynamics trajectories, and so on. The archive file can bewritten in TINKER format, or in formats usable with MSI's InsightII (their CAR file with .msiextension)orwithXMakemol(theirfileformatwith.xmolextension).OnlyactiveatomsarewrittenintotheInsightIIandXMakemoloutputfiles,allowingdisplayofpartialstructures.TheprogramcanalsoextractindividualcyclefilesfromaTINKERarchive. CORRELATE A program to compute time correlation functions from collections of TINKER cycle files. Its userequiresausersuppliedfunctionpropertythatcomputesthevalueofthepropertyforwhichatimecorrelationisdesiredfortwoinputstructures.Asampleroutineissuppliedthatcomputeseitheravelocityautocorrelationfunctionoranrmsstructuralsuperpositionasafunctionoftime.Themainbodyoftheprogramorganizestheoverallcomputationinanefficientmannerandoutputsthefinaltimecorrelationfunction. CRYSTAL A program for the manipulation of crystal structures including interconversion of fractional andCartesian coordinates, generation of the unit cell from an asymmetric unit, and building of acrystallineblockofspecifiedsizeviareplicationofasingleunitcell.Thepresentversioncanhandleabout25ofthemostcommonspacegroups,otherscaneasilybeaddedasneededbymodificationoftheroutinesymmetry. DIFFUSE Aprogramtocomputetheself-diffusionconstantforahomogeneousliquidviatheEinsteinequation.Apreviouslysaveddynamicstrajectoryisreadinand``unfolded''toreversetranslationofmoleculesduetouseofperiodicboundaryconditions.Theaveragemotionoverallmoleculesisthenusedtocomputetheself-diffusionconstant.Whilethecurrentprogramassumesahomogeneoussystem,itshouldbeeasytomodifythecodetohandlediffusionofindividualmoleculesorotherdesiredeffects. DISTGEOM Aprogramtoperformdistancegeometrycalculationsusingvariationsontheclassicmetricmatrixmethod.Auserspecifiednumberof structuresconsistentwithkeyfile inputdistanceanddihedralrestraintsisgenerated.Bondlengthandanglerestraintsarederivedfromtheinputstructure.Trialdistancesbetweenthetrianglesmoothedlowerandupperboundscanbechosenviaanyofseveralmetrizationmethods,includingaveryeffectivepartialrandompairwisescheme.Thecorrectradiusof gyration of the structure isautomaticallymaintainedby choosing trial distances fromGaussiandistributionsofappropriatemeanandwidth.Theinitialembeddedstructurescanbefurtherrefined


against a geometric restraint-only potential using either a sequential minimization protocol orsimulatedannealing. DOCUMENT TheDOCUMENTprogramisprovidedasaminimallistinganddocumentationtool.ItoperatesontheTINKERsourcecode,eitherindividualfilesorthecompletesourcelistingproducedbythecommandscriptlisting.make,togeneratelistsofroutines,commonblocksorvalidkeywords.Inaddition,the program has the ability to output a formatted parameter listing from the standard TINKERparameterfiles. INTEDIT Aprogramtoallowinteractiveinspectionandalterationof the internal coordinatedefinitionsandvaluesofaTINKERstructure.If thestructureisaltered,theuserhastheoptiontowriteoutanewinternalcoordinatesfileuponexit. INTXYZ A program to convert a TINKER .int internal coordinates formatted file into a TINKER .xyzCartesiancoordinatesformattedfile. NUCLEIC Aprogramforautomatedbuildingofnucleicacidstructures.Uponinteractiveinputofanucleotidesequence with optional phosphate backbone angles, the program builds internal and Cartesiancoordinates. Standard bond lengths and angles are used. Both DNA and RNA sequences aresupported as areA-, B- and Z-form structures.Double helixes of complementary sequencecan beautomaticallyconstructedviaarigiddockingofindividualstrands. PDBXYZ A program for converting aBrookhaven Protein DataBank file (a PDB file) into a TINKER.xyzCartesian coordinate file. If the PDB file contains only protein/peptide amino acid residues, thenstandardproteinconnectivityisassumed,andtransferredtothe.xyzfile.Fornon-proteinportionsofthePDB file, atomconnectivityisdeterminedby theprogrambasedon interatomicdistances.Theprogramalso has theability toadd or removehydrogen atoms froma proteinas required by theforcefieldspecifiedduringthecomputation. POLARIZE A program for computing molecular polarizability from an atom-based distributed model ofpolarizability.AdampedinteractionmodelduetoTholeisoptionallyviakeyfilesettings.ATINKER.xyz file isrequiredasinput.Theoutputconsistsoftheoverallpolarizabilitytensorintheglobalcoordinatesanditseigenvalues. PRMEDIT AprogramforformattingandrenumberingTINKERforcefieldparameterfiles.Whenatomtypesorclassesareadded toaparameter file, thisutilityprogramhas theability to renumberall theatomrecords sequentially, and alter type and class numbers in all other parameter entries tomaintainconsistency.


PROTEIN Aprogram forautomatedbuildingofpeptideandproteinstructures.Upon interactive inputofanaminoacidsequencewithoptionalphi/psi/omega/chiangles,D/Lchirality,etc.,theprogrambuildsinternalandCartesiancoordinates.Standardbondlengthsandanglesareassumedforthepeptide.Theprogramwilloptionallyconvertthestructuretoacyclicpeptide,oraddeitherorbothN-andC-terminalcappinggroups.Atomtypenumbersareautomaticallyassignedforthespecifiedforcefield.Thefinalcoordinatesandasequencefileareproducedastheoutput. RADIAL A program to compute the pair radial distribution function between two atom types. The usersuppliesthetwoatomnamesforwhichthedistributionfunctionistobecomputed,andthewidthofthedistancebinsfordataanalysis.Apreviouslysaveddynamicstrajectoryisreadasinput.Therawradialdistributionandasplinesmoothedversionarethenoutputfromzerotoadistanceequaltohalftheminimumperiodicboxdimension.TheatomnamesarematchedtotheatomnamecolumnoftheTINKER.xyzfile,independentofatomtype. SPACEFILL A program to compute the volume and surface areas of molecules. Using a modified version ofConnolly'soriginalanalyticaldescriptionofthemolecularsurface,theprogramdetermineseitherthevanderWaals, accessible ormolecular (contact/reentrant) volumeand surfacearea. Bothsurfaceareaandvolumearebrokendownintotheirgeometriccomponents,andsurfaceareaisdecomposedintotheconvexcontributionforeachindividualatom.Theproberadiusisinputasauseroption,andatomicradiicanbesetviathekeywordfile.IfTINKERarchivefilesareusedasinput,theprogramwillcomputethevolumeandsurfaceareaofeachstructureintheinputfile. SPECTRUM Aprogramtocomputeapowerspectrumfromvelocityautocorrelationdata.Asinput,thisprogramrequires a velocity autocorrelation function as produced by the CORRELATE program. This data,alongwithauserinputtimestep,areFouriertransformedtogeneratethespectralintensitiesoverawavelengthrange.Theresultisapowerspectrum,andthepositionsofthebandsarethosepredictedforaninfraredorRamanspectrum.However,thedataisnotweightedbymoleculardipolemomentderivativesaswouldberequiredtoproducecorrectIRintensities. SUPERPOSE Aprogramtosuperimposetwomolecularstructuresin3-dimensions.Avarietyofoptionsforinputof the atom sets to be usedduring the superposition are presented interactively to the user. Thesuperposition can be mass-weighted if desired, and the coordinates of the second structuresuperimposedonthefirststructureareoptionallyoutput.IfTINKERarchivefilesareusedasinput,theprogramwillcomputeallpairwisesuperpositionsbetweenstructuresintheinputfiles. SYBYLXYZ AprogramforconvertingaTRIPOSSybylMOL2file intoaTINKER.xyzCartesiancoordinatefile.ThecurrentversionoftheprogramdoesnotattempttoconverttheSybylatomstypesintotheactiveTINKERforcefieldtypes,i.e.,allatomstypesaresimplysettozero.


XYZEDIT A program that performs and of a variety of manipulations on an input TINKER .xyz Cartesiancoordinates formatted file. The present version of the program has the following interactivelyselectableoptions:(1)OffsettheNumbersoftheCurrentAtoms,(2)DeletionofIndividualSpecifiedAtoms, (3) Deletion of Specified Types of Atoms, (4)Deletion of Atoms outside Cutoff Range, (5)Insertion of Individual Specified Atoms, (6) Replace Old Atom Typewith aNewType, (7) AssignConnectivitiesbasedonDistance,(8)ConvertUnitsfromBohrstoAngstroms,(9)InvertthruOrigintogiveMirrorImage,(10)TranslateCenterofMasstotheOrigin,(11)TranslateaSpecifiedAtomtothe Origin, (12) Translate and Rotate to Inertial Frame, (13) Move to Specified Rigid BodyCoordinates, (14) Create and Fill a PeriodicBoundaryBox, (15) SoakCurrentMolecule inBox ofSolvent,(16)AppendanotherXYZfiletoCurrentOne.Inmostcases,multiplyoptionscanbeappliedsequentiallytoaninputfile.Attheendoftheeditingprocess,anewversionoftheoriginal.xyzfileiswrittenasoutput. XYZINT AprogramforconvertingaTINKER.xyzCartesiancoordinateformattedfile intoaTINKER.intinternalcoordinatesformattedfile.Thisprogramcanoptionallyuseanexistinginternalcoordinatesfileasatemplatefortheconnectivityinformation. XYZPDB AprogramforconvertingaTINKER.xyzCartesiancoordinatefileintoaBrookhavenProteinDataBankfile(aPDBfile). XYZSYBYL AprogramtoconvertaTINKER.xyzCartesiancoordinatesfileintoaTRIPOSSybylMOL2file.Theconversion generates only theMOLECULE, ATOM, BOND and SUBSTRUCTURE record type in theMOL2file.GenericSybylatomtypesareusedinmostcases;whiletheseatomtypesmayneedtobealteredinsomecases,SybylisusuallyabletocorrectlydisplaytheresultingMOL2file.


6. SpecialFeatures&Methods This section contains several short notes with further information about TINKER methodology,algorithmsandspecialfeatures.Thediscussionisnotintendedtobeexhaustive,butrathertoexplainfeaturesandcapabilitiessothatuserscanmakemorecompleteuseofthepackage. FileVersionNumbers AlloftheinputandoutputfiletypesroutinelyusedbytheTINKERpackagearecapableofexistingasmultipleversionsofabase filename.Forexample, if theprogramXYZINT is runon the input filemolecule.xyz, the output internal coordinates filewill bewritten to molecule.int. If a filenamedmolecule.intisalreadypresentpriortorunningXYZINT,thentheoutputwillbewritteninsteadtothenextavailableversion,inthiscasetomolecule.int_2.Infacttheoutputisgenerallywritten to the lowest available, previously unused version number (molecule.int_3,molecule.int_4, etc., as high as needed). Input file names are handled similarly. If simplymolecule ormolecule.xyz is entered as the input file name upon running XYZINT, then thehighestversionofmolecule.xyzwillbeusedastheactualinputfile.Ifanexplicitversionnumberisenteredaspartoftheinputfilename,thenthespecifiedversionwillbeusedastheinputfile. The versionnumber schemewill be recognized bymany older users as a holdover from theVMSoriginsofthefirstversionoftheTINKERsoftware.Ithasbeenmaintainedtomakeiteasiertochaintogethermultiplecalculations thatmaycreateseveralnewversionsofagiven file, and tomake itmoredifficult toaccidentlyoverwriteaneededresult.Theversionschemeapplies tomostusesofmany common TINKER file types such as .xyz, .int, .key, .arc. It is not used when anoverwrittenfile``update''isobviouslythecorrectaction,forexample,the.dynmoleculardynamicsrestart files. For those userswhoprefer amoreUnix-like operation, anddonot desire use of fileversions,thisfeaturecanbeturnedoffbyaddingtheNOVERSIONkeywordtotheapplicableTINKERkeyfile. The version scheme as implemented in TINKER does have two known quirks. First, it becomesimpossible to directly use the original unversioned copy of a file if higher version numbers arepresent. For example, if the files molecule.xyz and molecule.xyz_2 both exist, thenmolecule.xyzcannotbeaccessedasinputbyXYZINT.Ifmolecule.xyzisenteredinresponsetothe input file namequestion,molecule.xyz_2 (or the highest present versionnumber)will beusedas input.Theonlyworkaround is tocopyor renamemolecule.xyz to somethingelse, saymolecule.new,andusethatnamefortheinputfile.Secondly,missingversionnumbersalwaysendthe search for the highest available version number; i.e., version numbers are assumed to beconsecutive and without gaps. For example, if molecule.xyz, molecule.xyz_2 andmolecule.xyz_4arepresent,butnotmolecule.xyz_3,thenmolecule.xyz_2willbeusedasinputtoXYZINTifmoleculeisgivenastheinputfilename.Similarly,outputfileswillfillingapsinanalreadyexistingsetoffileversions. CommandLineOptions Manyoperatingsystemsorcompilersupplied-librariesmakeavailablesomethinglikethestandardUnix iargcandgetargroutines forcapturingcommand linearguments.On thesemachinesmostoftheTINKERprogramssupportaselectionofcommandlineargumentsandoptions.Thenameofthekeyfiletobeusedforacalculationisreadfromtheargumentfollowinga-k(equivalenttoeither-keyor-keyfile,caseinsensitive)commandlineargument.Notethatthe-koptionscanappearanywhereonthecommandlinefollowingtheexecutablename.Allothercommandlinearguments,excepting the nameof the executable program itself, are treated as input arguments. These input


argumentsarereadfromlefttorightandinterpretedinorderastheanswerstoquestionsthatwouldbe asked by an interactive invocation of the same TINKER program. For example, the followingcommandline: newton molecule -k test a a 0.01 willinvoketheNEWTONprogramonthestructurefilemolecule.xyzusingthekeyfiletest.key,automaticmode[a]forboththemethodandpreconditioning,and0.01fortheRMSgradientperatom termination criterion in kcal/mole/≈. Provided that the force field parameter set, etc. isprovided in test.key, the above compuation will procede directly from the command lineinvocationwithoutfurtherinteractiveinput. UseonMicrosoftWindowsSystems TINKER executables forMicrosoft PC systems should be run from the DOS or Command PromptwindowavailableunderthevariousversionsofWindows.TheTINKERexecutabledirectoryshouldbeaddedtoyourpathviatheautoexec.batfileorsimilar.IfusingWin2000orXP,setthenumberofscrollablelinesintheCommandPromptwindowtoaverylargenumber,sothatyouwillbeabletoinspect screen outputafter it flies by.WithWin95/98, these CommandPromptwindowsare onlyabletoscrollasmallnumberoflines(amazing!),soTINKERprogramswhichgeneratelargeamountsofscreenoutputshouldberunsuchthatoutputwillberedirectedtoafile.Thiscanbeaccomplishedbyrunning theTINKERprogram inbatchmodeorbyusing theUnix-likeoutput redirectionbuildintoDOS.Forexample,thecommand: dynamic < molecule.inp > molecule.log willruntheTINKERdynamicprogramtakinginputfromthefilemolecule.inpandsendingoutputtomolecule.log.AlsonotethatcommandlineoptionsasdescribedaboveareavailablewiththedistributedTINKERexecutables. Anotheralternative,particularlyattractivetothosealreadyfamiliarwithLinuxorUnixsystems,istodownload the Cygwin package currently available under GPL license from the sitehttp://source.redhat.com/cygwin/. The cygwin tools provide many of the GNU tools,includingabashshellwindowfromwhichTINKERprogramscanberun. If the distributed TINKER executables are run directly fromWindows by double clicking on theprogram icon, then the program will run in its own window. However, upon completion of theprogram the window will close and screen output will be lost. Any output files written by theprogramwill,ofcourse,stillbeavailable.TheWindowsbehaviorcanbechangedbyaddingtheEXIT-PAUSEkeyword to thekeyfile.Thiskeywordcauses theexecutationwindowto remainopenaftercompletionuntilthe``Enter''keyispressed. UseonAppleMacintoshSystems TheTINKER executables are best rununderMacOSX in a ``terminal'' applicationwindowwherebehaviorisidenticaltothatinaLinuxterminal.AtpresenttheForceFieldExplorerGUIforTINKERwillnotrunonOSXsincetherequiredJava3Dextensionsareunavailable. WehavediscontinuedactivesupportforMacOS9.However,theOS9versionsofTINKERarerunbydoubleclickingonaprogram icon.Theprogramwill run in itsownwindowtowhichall ``screen''outputwillbedirected.Uponprogramtermination thewindowwill remainactivependinga finalreturnenteredbytheuserwhichwillclosethewindow.Priortothefinalreturn,thecontentsofthescreenwindowcanbesavedtoafileviatheclipboardforpermanentstorage.NotethatMacintosh


OS9usesacoloninsteadofaforward-orback-slashasthedirectoryseparator,sokeyfilestransferedfromothermachineswillneedtobealteredaccordingly. AtomTypesvs.AtomClasses Manipulationofatomtypesandtheproliferationofparametersasatomsarefurthersubdividedintonew types is the bane of force field calculation. For example, if each topologically distinct atomarisingfromthe20naturalaminoacidsisgivenadifferentatomtype,thenabout300separatetypeare required (this ignores the different N- and C-terminal forms of the residues, diastereotopichydrogens, etc.). However, all these types lead to literally thousands of different force fieldparameters.Infact,therearemanythousandsofdistincttorsionalparametersalone.Itisimpossibleat present to fully optimize each of these parameters; and even ifwe could, a greatmany of theparameters would be nearly identical. Two somewhat complimentary solutions are available tohandle the proliferation of parameters. The first is to specify themolecular fragments towhichagiven parameter can be applied in terms of a chemical structure language, SMILES strings forexample.Somecommercialsystems,suchastheTRIPOSSybylsoftware,makeuseofsuchaschemetoparsestructuresandassignforcefieldparameters. A second general approach is to use hierarchical cascades of parameter groups. TINKER uses asimpleversionofthisscheme.EachTINKERforcefieldatomhasbothanatomtypenumberandanatomclassnumber.Thetypesaresubsetsoftheatomclasses, i.e.,severaldifferentatomtypescanbelong to the same atom class. Force field parameters that are somewhat less sensitive to localenvironment, such as local geometry terms,are thenprovided and assignedbased on atom class.Otherenergyparameters,suchaselectrostaticparameters,thatareveryenvironmentdependentareassigned over the atom types. This greatly reduces the number of independent multiple-atomparameterslikethefour-atomtorsionalparameters. CalculationsonPartialStructures Twomethodsareavailableforperformingenergeticcalculationsonportionsorsubstructureswithina fullmolecular system.TINKERallowsdivisionof theentiresystemintoactive and inactivepartswhichcanbedefinedviakeywords.Insubsequentcalculations,suchasminimizationordynamics,only theactiveportionsof thesystemareallowed tomove.The forcefieldengineresponds to theactive/inactivedivisionbycomputingallenergeticinteractionsinvolvingatleastoneactiveatom;i.e.,anyinteractionwhoseenergycanchangewiththemotionofoneormoreactiveatomsiscomputed. Thesecondmethodforpartialstructurecomputationinvolvesdividingtheoriginalsystemintoasetofatomgroups.Asbefore,thegroupscanbespecifiedviaappropriatekeywords.ThecurrentTINKERimplementationallowsspecificationofuptoamaximumnumberofgroupsasgiveninthesizes.idimensioningfile.Thegroupsmustbedisjoint inthatnoatomcanbelongtomorethanonegroup.Furtherkeywordsallowtheusertospecifywhichintra-andintergroupsetsofenergeticinteractionswillcontributetothetotalforcefieldenergy.Weightsforeachsetofinteractionsinthetotalenergycanalsobeinput.Aspecificenergeticinteractionisassignedtoaparticularintra-orintergroupsetifall the atoms involved in the interaction belong to the group (intra-) or pair of groups (inter-).Interactionsinvolvingatomsfrommorethantwogroupsarenotcomputed. Note that thegroupsmethod and active/inactivemethoduse different assignment procedures forindividualinteractions.Theactive/inactiveschemeisintendedforsituationswhereonlyaportionofa system is allowed tomove, but the total energy needs to reflect the presence of the remaininginactiveportionofthestructure.Thegroupsmethodis intendedforuseinrigidbodycalculations,andisneededforcertainkindsoffreeenergyperturbationcalculations. MetalComplexesandHypervalentSpecies


ThedistributionversionofTINKERcomesdimensionedforamaximumatomiccoordinationnumberof four as needed for standard organic compounds. In order to use TINKER for calculations onspeciescontaininghighercoordinationnumbers,simplychangethevalueoftheparametermaxvalin themasterdimensioning filesizes.i andrebuilt thepackage.Note that thisparametervalueshouldnotbesetlargerthannecessarysincelargevaluescanslowtheexecutionofportionsofsomeTINKERprograms. Manymolecularmechanicsapproachestoinorganicandmetalstructuresuseananglebendingtermwhich is softer than theusualharmonicbendingpotential.TINKER implementsaFourierbendingterm similar to that used by the Landis group's SHAPES force field. The parameters for specificFourierangletermsaresuppliedviatheANGLEFparameterandkeywordformat.NotethataFouriertermwillonlybeusedforaparticularangleifacorrespondingharmonicangletermisnotpresentintheparameterfile. WearenowcollaboratingwithAndersCarlsson'sgroupinSt.LouistoaddhistransitionmetalligandfieldtermtoTINKER.SupportforthisadditionalpotentialfunctionalformisalreadyintheTINKERsourcecode,andweplantoreleasetheenergyroutinesafterfurthertestingandparameterization. NeighborMethodsforNonbondedTerms In addition to standarddouble loopmethods, theMethod of Lights isavailable to speedneighborsearching. Thismethod based on taking intersections of sorted atom lists can bemuch faster forproblemswherethecutoffdistanceissignificantlysmallerthanhalfthemaximalcelldimension.ThecurrentversionofTINKERdoesnotimplementthe``neighborlist''schemescommontomanyothersimulationpackages. PeriodicBoundaryConditions Both spherical cutoff images or replicates of a cell are supported by all TINKER programs thatimplementperiodicboundaryconditions.Wheneverthecutoffdistanceistoolargefortheminimumimagetobetheonlyrelevantneighbor(i.e.,halftheminimumboxdimensionfororthogonalcells),TINKERwillautomaticallyswitchfromtheimageformalismtouseofreplicatedcells. DistanceCutoffsforEnergyFunctions Polynomialenergyswitchingoverawindowisusedfortermswhoseenergyissmallnearthecutoffdistance.Formonopoleelectrostaticinteractions,whicharequitelargeintypicalcutoffranges,atwopolynomialmultiplicative-additiveshiftedenergyswitchuniquetoTINKERisapplied.TheTINKERmethodissimilarinspirittotheforceswitchingmethodsofSteinbachandBrooks,J.Comput.Chem.,15, 667-683 (1994).While the particlemeshEwaldmethod is preferredwhenperiodic boundaryconditionsarepresent,TINKER'sshiftedenergyswitchwithreasonableswitchingwindowsisquitesatisfactory for most routine modeling problems. The shifted energy switch minimizes theperturbationoftheenergyandthegradientatthecutofftoacceptablelevels.Problemsshouldariseonly if the property you wish to monitor is known to require explicit inclusion of long rangecomponents(i.e.,calculationofthedielectricconstant,etc.). EwaldSummationsMethods TINKER contains a versions of the Ewald summation technique for inclusion of long rangeelectrostatic interactions via periodic boundaries. The particle mesh Ewald (PME) method isavailableforsimplecharge-chargepotentials,whileregularEwaldisprovidedforpolarizableatomicmultipoleinteractions.TheaccuracyandspeedoftheregularandPMEcalculationsisdependenton


several interrelated parameters. For both methods, the Ewald coefficient and real-space cutoffdistance must be set to reasonable and complementary values. Additional control variables forregularEwaldarethefractionalcoverageandnumberofvectorsusedinreciprocalspace.ForPMEtheadditional controlvaluesare theB-splineorderandchargegriddimensions.CompletecontroloveralloftheseparametersisavailableviatheTINKERkeyfilemechanism.BydefaultTINKERwillselectasetofparameterswhichprovideareasonablecompromisebetweenaccuracyandspeed,buttheseshouldbecheckedandmodifiedasnecessaryforeachindividualsystem. ContinuumSolvationModels Several alternative continuum solvation algorithms are containedwithinTINKER.All of these areaccessed via the SOLVATE keyword and its modifiers. Two simple surface area methods areimplemented: theASPmethodofEisenbergandMcLachlan,and theSASAmethod fromScheraga'sgroup.Thesemethodsareapplicable toanyof thestandardTINKER force fields.Variousschemesbased on the generalizedBorn formalism are also available: the original 1990numerical `Ònion-shell'' GB/SA method from Still's group, the 1997 analytical GB/SA method also due to Still, apairwise descreening algorithm originally proposed by Hawkins, Cramer and Truhlar, and theanalytical continuum solvation (ACE)method of Schaefer andKarplus. At present, thegeneralizedBorn methods should only be used with force fields having simple partial charge electrostaticinteractions. SomefurthercommentsareinorderregardingtheGB/SA-stylesolvationmodels.The`Ònion-shell''model is provided mostly for comparison purposes. It uses an exact, analytical surface areacalculation for the cavity term and the numerical scheme described in the original paper for thepolarizationterm.Thismethodisveryslow,especiallyfor largesystems,anddoesnotcontainthecontributionoftheBornradiichainruletermtothefirstderivatives.Werecommenditsuseonlyforsingle-point energy calculations. The other GB/SA methods (`ànalytical'' Still, H-C-T pairwisedescreening, and ACE) use an approximate cavity term based on Born radii, and do contain fullycorrectderivativesincludingtheBornradiichainrulecontribution.ThesemethodsallscaleinCPUtime with the square of the size of the system, and can be used with minimization, moleculardynamicsandlargemolecules. Finally,wenotethattheACEsolvationmodelshouldnotbeusedwiththecurrentversionofTINKER.Thealgorithmisfully implementedinthesourcecode,butparameterizationisnotcomplete.Asoflate 2000, parameter values are only available in the literature for use of ACE with the olderCHARMM19forcefield.Weplantodevelopvaluesforusewithmoremodernall-atomforcefields,andthesewillbeincorporatedintoTINKERsometimeinthefuture. PolarizableMultipoleElectrostatics Atomicmultipoleelectrostaticsthroughthequadrupolemomentissupportedbythecurrentversionof TINKER, as is either mutual or direct dipole polarization. Ewald summation is available forinclusion of long range interactions. Calculations are implemented via a mixture of the CCP5algorithms of W. Smith and the Applequist-Dykstra Cartesian polytensor method. At presentanalyticalenergyandCartesiangradientcodeisprovided. TheTINKERpackageallowsintramolecularpolarizationtobetreatedviaaversionoftheinteractiondampingschemeofThole.ToimplementtheTholescheme,itisnecessarytosetallthemutual-1x-scale keywords to a value of one. The other polarization scaling keyword series,direct-1x-scale andpolar-1x-scale, can be set independently to enableawide variety of polarizationmodels. In order to use an Applequist-style model without polarization damping, simply set thepolar-dampkeywordtozero.


PotentialEnergySmoothing VersionsofourPotentialSmoothingandSearch(PSS)methodologyhavebeenimplementedwithinTINKER.ThismethodsbelongtothesamegeneralfamilyasScheraga'sDiffusionEquationMethod,Straub's Gaussian Density Annealing, Shalloway's Packet Annealing and Verschelde's EffectiveDiffusedPotential,butouralgorithmsreflectourownongoingresearchinthisarea.Inmanywaysthe TINKER potential smoothing methods are the deterministic analog of stochastic simulatedannealing. The PSS algorithms are very powerful, but are relatively new and are still undergoingmodification,testingandcalibrationwithinourresearchgroup.ThisversionofTINKERalsoincludesa basin-hopping conformational scanning algorithm in the program SCAN which is particularlyeffectiveonsmoothedpotentialsurfaces. DistanceGeometryMetrization Amuchimprovedandveryfastrandompairwisemetrizationschemeisavailablewhichallowsgoodsampling during trial distancematrix generationwithout the usual structural anomalies and CPUconstraints of othermetrization procedures. An outline of themethodology and its application toNMRNOE-basedstructurerefinementisdescribedinthepaperbyHodsdon,etal.inJ.Mol.Biol.,264,585-602(1996).Wehaveobtainedgoodresultswithsomething like thekeywordphrasetrial-distribution pairwise 5, which performs 5% partial random pairwise metrization. Forstructuresoverseveralhundredatoms,avaluelessthan5forthepercentageofmetrizationshouldbefine.


7. UseoftheKeywordControlFile UsingKeywordstoControlTINKERCalculationsThissectioncontainsadescriptionoftheover300keywordparameterswhichmaybeusedtodefineoralterthecourseofaTINKERcalculation.Thekeywordcontrolfileisoptionalinthesensethatallof theTINKERprogramswill run in theabsenceofakeyfileandwill simplyusedefaultvaluesorquery the user for needed information. However, the keywords allow use of a wide variety ofalgorithmicandproceduraloptions,manyofwhichareunavailableinteractively. Keywordsarereadfromthekeywordcontrolfile.Allprogramslookfirstforakeyfilewiththesamebasenameastheinputmolecularsystemandendingintheextension.key.Ifthisfiledoesnotexist,then TINKER tries to use a generic keyfilewith the nametinker.key and located in the samedirectoryas theinput system.Ifneithera system-specificnoragenerickeyfile ispresent,TINKERwill continue by using default values for keyword options and asking interactive questions asnecessary. TINKERsearches thekeyfileduring thecourseofa calculation for relevantkeywords thatmaybepresent.Allkeywordsmustappearas the firstwordon the line.Anyblankspace to the leftof thekeyword is ignored, and all contents of the keyfiles are case insensitive. Some keywords takemodifiers;i.e.,TINKERlooksfurtheronthesamelineforadditionalinformation,suchasthevalueofsomeparameter related to the keyword.Modifier information is read in free format, butmust becompletely contained on the same line as the originalkeyword. Any lines contained in the keyfilewhichdonotqualifyasvalidkeywordlinesaretreatedascommentsandaresimplyignored. Severalkeywordstakea listof integervalues(atomnumbers, forexample)asmodifiers.Forthesekeywordstheintegerscansimplybelistedexplicitlyandseparatedbyspaces,commasortabs.Ifarange of numbers is desired, it can be specified by listing the negative of the first number of therange, followed by a separator and the last number of the range. For example, the keyword lineACTIVE 4 -9 17 23couldbeusedtoaddatoms4,9through17,and23tothesetofactiveatomsduringaTINKERcalculation. KeywordsGroupedbyFunctionality ListedbelowaretheavailableTINKERkeywordssortedintogroupsbygeneralfunction.Thesectionendswithanalphabeticallistcontainingeachindividualkeyword,alongwithabriefdescriptionofitsaction,possiblekeywordmodifiers,andusageexamples. OUTPUTCONTROLKEYWORDS ARCHIVE DEBUG DIGITS ECHO EXIT-PAUSE NOVERSIONOVERWRITE PRINTOUT SAVE-CYCLESAVE-FORCE SAVE-INDUCED SAVE-VELOCITYVERBOSE WRITEOUT FORCEFIELDSELECTIONKEYWORDS FORCEFIELD PARAMETERS POTENTIALFUNCTIONSELECTIONKEYWORDS


ANGANGTERM ANGLETERM BONDTERM CHARGETERM CHGDPLTERM DIPOLETERM EXTRATERM IMPROPTERM IMPTORSTERMMETALTERM MPOLETERM OPBENDTERMOPDISTTERM PITORSTERM POLARIZETERM RESTRAINTERM RXNFIELDTERM SOLVATETERMSTRBNDTERM STRTORTERM TORSIONTERMTORTORTERM UREYTERM VDWTERM POTENTIALFUNCTIONPARAMETERKEYWORDS ANGANG ANGLE ANGLE3 ANGLE4 ANGLE5 ANGLEF ATOM BIOTYPE BOND BOND3 BOND4 BOND5 CHARGE DIPOLE DIPOLE3 DIPOLE4 DIPOLE5 ELECTNEG HBOND IMPROPER IMPTORSMETAL MULTIPOLE OPBEND OPDIST PIATOM PIBOND PITORS POLARIZE SOLVATESTRBND STRTORS TORSIONTORSION4 TORSION5 TORTORUREYBRAD VDW VDW14 VDWPR ENERGYUNITCONVERSIONKEYWORDS ANGLEUNIT ANGANGUNIT BONDUNIT ELECTRIC IMPROPUNIT IMPTORUNITOPBENDUNIT OPDISTUNIT PITORSUNITSTRBNDUNIT STRTORUNIT TORSIONUNITTORTORUNIT UREYUNIT LOCALGEOMETRYFUNCTIONALFORMKEYWORDS ANGLE-CUBIC ANGLE-QUARTIC ANGLE-PENTIC ANGLE-SEXTIC BOND-CUBIC BOND-QUARTICBONDTYPE MM2-STRBND PISYSTEM UREY-CUBIC UREY-QUARTIC VANDERWAALSFUNCTIONALFORMKEYWORDS A-EXPTERM B-EXPTERM C-EXPTERM DELTA-HALGREN EPSILONRULE GAMMA-HALGRENGAUSSTYPE RADIUSRULE RADIUSSIZERADIUSTYPE VDW-12-SCALE VDW-13-SCALE VDW-14-SCALE VDW-15-SCALE VDW-CORRECTIONVDWINDEX VDWTYPE ELECTROSTATICSFUNCTIONALFORMKEYWORDS CHG-12-SCALE CHG-13-SCALE CHG-14-SCALE


CHG-15-SCALE CHG-BUFFER DIELECTRICDIRECT-11-SCALE DIRECT-12-SCALE DIRECT-13-SCALEDIRECT-14-SCALE MPOLE-12-SCALE MPOLE-13-SCALEMPOLE-14-SCALE MPOLE-15-SCALE MUTUAL-11-SCALEMUTUAL-12-SCALE MUTUAL-13-SCALE MUTUAL-14-SCALEPOLAR-12-SCALE POLAR-13-SCALE POLAR-14-SCALEPOLAR-15-SCALE POLAR-ASPC POLAR-EPSPOLAR-SOR POLARIZATION REACTIONFIELD NONBONDEDCUTOFFKEYWORDS CHG-CUTOFF CHG-TAPER CUTOFF DPL-CUTOFF DPL-TAPER HESS-CUTOFF LIGHTS MPOLE-CUTOFF MPOLE-TAPER NEIGHBOR-GROUPS NEUTRAL-GROUPS POLYMER-CUTOFF TAPER TRUNCATE VDW-CUTOFF VDW-TAPER EWALDSUMMATIONKEYWORDS EWALD EWALD-ALPHA EWALD-BOUNDARYEWALD-CUTOFF PME-GRID PME-ORDER CRYSTALLATTICE&PERIODICBOUNDARYKEYWORDS A-AXIS B-AXIS C-AXIS ALPHA BETA GAMMA NO-SYMMETRY OCTAHEDRON SPACEGROUPX-AXIS Y-AXIS Z-AXIS NEIGHBORLISTKEYWORDS CHG-LIST LIST-BUFFER MPOLE-LISTNEIGHBOR-LIST VDW-LIST OPTIMIZATIONKEYWORDS ANGMAX CAPPA FCTMIN HGUESS INTMAX LBFGS-VECTORSMAXITER NEWHESS NEXTITERSLOPEMAX STEEPEST-DESCENT STEPMAXSTEPMIN MOLECULARDYNAMICSKEYWORDS BEEMAN-MIXING DEGREES-FREEDOM INTEGRATORREMOVE-INERTIA THERMOSTAT&BAROSTATKEYWORDS ANISO-PRESSURE BAROSTAT COLLISIONCOMPRESS FRICTION FRICTION-SCALINGTAU-PRESSURE TAU-TEMPERATURE THERMOSTAT


VOLUME-MOVE VOLUME-SCALE VOLUME-TRIAL TRANSITIONSTATEKEYWORDS DIVERGE GAMMAMIN REDUCE SADDLEPOINT DISTANCEGEOMETRYKEYWORDS TRIAL-DISTANCE TRIAL-DISTRIBUTION VIBRATIONALANALYSISKEYWORDS IDUMP VIB-ROOTS VIB-TOLERANCE IMPLICITSOLVATIONKEYWORDS BORN-RADIUS GK-RADIUS GKCGKR SOLVENT-PRESSURE SURFACE-TENSION POISSON-BOLTZMANNKEYWORDS AGRID APBS-GRID BCFLCGCENT CGRID FGCENTFGRID ION MG-AUTOMG-MANUAL PB-RADIUS PDIESDENS SDIE SMINSRAD SRFM SWIN MATHEMATICALALGORITHMKEYWORDS FFT-PACKAGE RANDOMSEED PARALLELIZATIONKEYWORDS OPENMP-THREADS FREEENERGYPERTURBATIONKEYWORDS CHG-LAMBDA DPL-LAMBDA LAMBDALIGAND MPOLE-LAMBDA MUTATEPOLAR-LAMBDA VDW-LAMBDA PARTIALSTRUCTUREKEYWORDS ACTIVE GROUP GROUP-INTER GROUP-INTRA GROUP-MOLECULE GROUP-SELECTINACTIVE CONSTRAINT&RESTRAINTKEYWORDS BASIN ENFORCE-CHIRALITY RATTLE RATTLE-DISTANCE RATTLE-EPS RATTLE-LINERATTLE-ORIGIN RATTLE-PLANE RESTRAIN-ANGLE


RESTRAIN-DISTANCE RESTRAIN-GROUPS RESTRAIN-POSITIONRESTRAIN-TORSION SPHERE WALL PARAMETERFITTINGKEYWORDS FIT-ANGLE FIT-BOND FIT-OPBENDFIT-STRBND FIT-TORSION FIT-UREYFIX-ANGLE FIX-BOND FIX-DIPOLEFIX-MONOPOLE FIX-OPBEND FIX-QUADRUPOLEFIX-STRBND FIX-TORSION FIX-UREYPOTENTIAL-ATOMS POTENTIAL-FIT POTENTIAL-OFFSETPOTENTIAL-SHELLS POTENTIAL-SPACING TARGET-DIPOLETARGET-QUADRUPOLE POTENTIALSMOOTHINGKEYWORDS DEFORM DIFFUSE-CHARGE DIFFUSE-TORSION DIFFUSE-VDW SMOOTHING DescriptionofIndividualKeywords The following isanalphabetical listof theTINKERkeywordsalongwithabriefdescriptionof theactionofeachkeywordandrequiredoroptionalparametersthatcanbeusedtoextendormodifyeachkeyword.Theformatofpossiblemodifiers,ifany,isshowninbracketsfollowingeachkeyword. A-AXIS[real]Setsthevalueofthea-axislengthforacrystalunitcell,or,equivalently,theX-axislengthforaperiodicbox.ThelengthvalueinAngstromsislistedafterthekeyword. A-EXPTERM[real]Setsthevalueofthe``A''premultipliertermintheBuckinghamvanderWaalsfunction,i.e.,thevalueofAintheformulaEvdw=e{Aexp[-B(Ro/R)]-C(Ro/R)6}. ACTIVE [integer list] Sets the list of active atoms during a TINKER computation. Individualpotential energy terms are computedwhen at least one atom involved in the term is active. ForCartesian space calculations, active atoms are those allowed to move. For torsional spacecalculations,rotationsareallowedwhenallatomsononesideoftherotatedbondareactive.MultipleACTIVElinescanbepresentinthekeyfileandaretreatedcumulatively. Oneachlinethekeywordcanbefollowedbyoneormoreatomnumbersoratomranges.ThepresenceofanyACTIVEkeywordoverridesanyINACTIVEkeywordsinthekeyfile. ALPHA[real]Setsthevalueoftheaangleofacrystalunitcell,i.e.,theanglebetweentheb-axisandc-axisofaunitcell,or,equivalently,theanglebetweentheY-axisandZ-axisofaperiodicbox.ThedefaultvalueintheabsenceoftheALPHAkeywordis90degrees. ANGANG[1integer&3reals] Thiskeywordprovidesthevaluesforasingleangle-anglecrosstermpotentialparameter. ANGANGTERM[NONE/ONLY]Thiskeywordcontrolsuseoftheangle-anglecrosstermpotentialenergy.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONEoption turns off use of this potential energy term. TheONLYoption turns off all potential energytermsexceptforthisone.


ANGANGUNIT[real] Sets thescale factorneeded toconvert theenergyvaluecomputedby theangle-anglecrosstermpotential intounitsofkcal/mole.Thecorrectvalueis forcefielddependentandtypicallyprovidedintheheaderofthemasterforcefieldparameterfile.Thedefaultof(p/180)2=0.0003046isused,iftheANGANGUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. ANGLE[3integers&4reals]Thiskeywordprovidesthevaluesforasinglebondanglebendingparameter.Theintegermodifiersgivetheatomclassnumbersforthethreekindsofatomsinvolvedintheanglewhichistobedefined.Therealnumbermodifiersgivetheforceconstantvaluefortheangleanduptothreeidealbondanglesindegrees.Inmostcasesonlyoneidealbondangleisgiven,and that value is used for all occurrences of the specified bond angle. If all three ideal anglesaregiven,thevaluesapplywhenthecentralatomoftheangleisattachedto0,1or2additionalhydrogenatoms, respectively. This ``hydrogen environment'' option is provided to implement thecorresponding feature of Allinger's MM force fields. The default units for the force constant arekcal/mole/radian2,butthiscanbecontrolledviatheANGLEUNITkeyword. ANGLE-CUBIC[real] SetsthevalueofthecubictermintheTaylorseriesexpansionformofthebondanglebendingpotentialenergy.Therealnumbermodifiergivesthevalueofthecoefficientasamultiple of the quadratic coefficient. This term multiplied by the angle bending energy unitconversionfactor,theforceconstant,andthecubeofthedeviationofthebondanglefromitsidealvaluegivesthecubiccontributiontotheanglebendingenergy.ThedefaultvalueintheabsenceoftheANGLE-CUBICkeywordiszero;i.e.,thecubicanglebendingtermisomitted. ANGLE-PENTIC[real]SetsthevalueofthefifthpowertermintheTaylorseriesexpansionformofthebondanglebendingpotentialenergy.Therealnumbermodifiergivesthevalueofthecoefficientas a multiple of the quadratic coefficient. This termmultiplied by the angle bending energy unitconversionfactor,theforceconstant,andthefifthpowerofthedeviationofthebondanglefromitsideal value gives the pentic contribution to the angle bending energy. The default value in theabsenceoftheANGLE-PENTICkeywordiszero;i.e.,thepenticanglebendingtermisomitted. ANGLE-QUARTIC[real]SetsthevalueofthequartictermintheTaylorseriesexpansionformofthebondanglebendingpotentialenergy.Therealnumbermodifiergivesthevalueofthecoefficientas a multiple of the quadratic coefficient. This termmultiplied by the angle bending energy unitconversionfactor,theforceconstant,andtheforthpowerofthedeviationofthebondanglefromitsideal value gives the quartic contribution to the angle bending energy. The default value in theabsenceoftheANGLE-QUARTICkeywordiszero;i.e.,thequarticanglebendingtermisomitted. ANGLE-SEXTIC[real]SetsthevalueofthesixthpowertermintheTaylorseriesexpansionformofthebondanglebendingpotentialenergy.Therealnumbermodifiergivesthevalueofthecoefficientas a multiple of the quadratic coefficient. This termmultiplied by the angle bending energy unitconversionfactor,theforceconstant,andthesixthpowerofthedeviationofthebondanglefromitsidealvaluegivesthesexticcontributiontotheanglebendingenergy.ThedefaultvalueintheabsenceoftheANGLE-SEXTICkeywordiszero;i.e.,thesexticanglebendingtermisomitted. ANGLE3[3integers&4reals]Thiskeywordprovidesthevaluesforasinglebondanglebendingparameterspecifictoatomsin3-memberedrings.Theintegermodifiersgivetheatomclassnumbersforthethreekindsofatomsinvolvedintheanglewhichistobedefined.Therealnumbermodifiersgivetheforceconstantvaluefortheangleanduptothreeidealbondanglesindegrees.Ifallthreeidealanglesaregiven,thevaluesapplywhenthecentralatomoftheangleisattachedto0,1or2additional hydrogen atoms, respectively. The default units for the force constant arekcal/mole/radian2,butthiscanbecontrolledviatheANGLEUNITkeyword.IfanyANGLE3keywordsarepresent,eitherinthemasterforcefieldparameterfileorthekeyfile,thenTINKERrequiresthat


special ANGLE3 parameters be given for all angles in 3-membered rings. In the absence of anyANGLE3keywords,standardANGLEparameterswillbeusedforbondsin3-memberedrings. ANGLE4[3integers&4reals]Thiskeywordprovidesthevaluesforasinglebondanglebendingparameterspecifictoatomsin4-memberedrings.Theintegermodifiersgivetheatomclassnumbersforthethreekindsofatomsinvolvedintheanglewhichistobedefined.Therealnumbermodifiersgivetheforceconstantvaluefortheangleanduptothreeidealbondanglesindegrees.Ifallthreeidealanglesaregiven,thevaluesapplywhenthecentralatomoftheangleisattachedto0,1or2additional hydrogen atoms, respectively. The default units for the force constant arekcal/mole/radian2,butthiscanbecontrolledviatheANGLEUNITkeyword.IfanyANGLE4keywordsarepresent,eitherinthemasterforcefieldparameterfileorthekeyfile,thenTINKERrequiresthatspecial ANGLE4 parameters be given for all angles in 4-membered rings. In the absence of anyANGLE4keywords,standardANGLEparameterswillbeusedforbondsin4-memberedrings. ANGLE5[3integers&4reals]Thiskeywordprovidesthevaluesforasinglebondanglebendingparameterspecifictoatomsin5-memberedrings.Theintegermodifiersgivetheatomclassnumbersforthethreekindsofatomsinvolvedintheanglewhichistobedefined.Therealnumbermodifiersgivetheforceconstantvaluefortheangleanduptothreeidealbondanglesindegrees.Ifallthreeidealanglesaregiven,thevaluesapplywhenthecentralatomoftheangleisattachedto0,1or2additional hydrogen atoms, respectively. The default units for the force constant arekcal/mole/radian2,butthiscanbecontrolledviatheANGLEUNITkeyword.IfanyANGLE5keywordsarepresent,eitherinthemasterforcefieldparameterfileorthekeyfile,thenTINKERrequiresthatspecial ANGLE5 parameters be given for all angles in 5-membered rings. In the absence of anyANGLE5keywords,standardANGLEparameterswillbeusedforbondsin5-memberedrings. ANGLEF[3integers&3reals]ThiskeywordprovidesthevaluesforasinglebondanglebendingparameterforaSHAPES-styleFourierpotential function.Theintegermodifiersgivetheatomclassnumbersforthethreekindsofatomsinvolvedintheanglewhichistobedefined.Therealnumbermodifiersgivetheforceconstantvaluefortheangle,theangleshift indegrees,andtheperiodicityvalue. Note that the force constant should be given as the ``harmonic'' value and not the nativeFourier value. The default units for the force constant are kcal/mole/radian2, but this can becontrolledviatheANGLEUNITkeyword. ANGLETERM [NONE/ONLY] This keyword controls use of the bond angle bending potentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONE option turns off use of this potential energy term. The ONLY option turns off all potentialenergytermsexceptforthisone. ANGLEUNIT[real]Setsthescalefactorneededtoconverttheenergyvaluecomputedbythebondangle bending potential into units of kcal/mole. The correct value is force field dependent andtypically provided in the header of the master force field parameter file. The default value of(p/180)2=0.0003046isused, if theANGLEUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. ANGMAX [real] Set themaximum permissible angle between the current optimization searchdirection and the negative of the gradient direction. If thismaximumangle value isexceeded, theoptimization routine will note an error condition and may restart from the steepest descentdirection. The default value in the absence of the ANGMAX keyword is usually 88 degrees forconjugategradientmethodsand180degrees(i.e.,disabled)forvariablemetricoptimizations. ANISO-PRESSURE This keyword invokes use of full anisotropic pressure during dynamicssimulations. When using this option, the three axis lengths and axis angles vary separately in


response to the pressure tensor.The default, in theabsence of the keyword, is isotropic pressurebasedontheaverageofthediagonalofthepressuretensor. ARCHIVEThiskeywordcausesTINKERmoleculardynamics-basedprogramstowritetrajectoriesdirectlytoasingleplain-textarchivefilewiththe.arc format.Ifanarchivefilealreadyexistsatthestartofthecalculation,thenthenewlygeneratedtrajectoryisappendedtotheendoftheexistingfile.The default in the absence of this keyword is to write the trajectory snapshots to consecutivelynumberedcyclefiles. ATOM[2 integers,name,quotedstring, integer, real& integer] Thiskeywordprovides thevaluesneededtodefineasingleforcefieldatomtype. B-AXIS[real]Setsthevalueoftheb-axislengthforacrystalunitcell,or,equivalently,theY-axislengthforaperiodicbox.ThelengthvalueinAngstromsislistedafterthekeyword.Ifthekeywordisabsent,theb-axislengthissetequaltothea-axislength. B-EXPTERM[real]Setsthevalueofthe``B''exponentialfactorintheBuckinghamvanderWaalsfunction,i.e.,thevalueofBintheformulaEvdw=e{Aexp[-B(Ro/R)]-C(Ro/R)6}. BAROSTAT[BERENDSEN] Thiskeywordselectsabarostatalgorithm foruseduringmoleculardynamics.Atpresentonlyonemodifierisavailable,aBerendsenbathcouplingmethod.ThedefaultintheabsenceoftheBAROSTATkeywordistousetheBERENDSENalgorithm. BASIN [2 reals] Presence of this keyword turns on a ``basin'' restraint potential function thatservestodrivethesystemtowardacompactstructure.TheactualfunctionisaGaussianoftheformEbasin=SAexp[-BR2],summedoverallpairsofatomswhereRisthedistancebetweenatoms.TheAandB values are the depth andwidth parameters given asmodifiers to theBASINkeyword. Thispotential is currently used to control the degree of expansion during potential energy smoothproceduresthroughtheuseofshallow,broadbasins. BETA[real]Setsthevalueofthebangleofacrystalunitcell,i.e.,theanglebetweenthea-axisandc-axisofaunitcell,or,equivalently,theanglebetweentheX-axisandZ-axisofaperiodicbox.ThedefaultvalueintheabsenceoftheBETAkeywordistosetthebangleequaltotheaangleasgivenbythekeywordALPHA. BIOTYPE[integer,name,quotedstring&integer]Thiskeywordprovidesthevaluestodefinethecorrespondencebetweenasinglebiopolymeratomtypeanditsforcefieldatomtype. BOND [2 integers& 2 reals] This keyword provides the values for a single bond stretchingparameter.Theintegermodifiersgivetheatomclassnumbersforthetwokindsofatomsinvolvedinthebondwhichistobedefined.Therealnumbermodifiersgivetheforceconstantvalueforthebondandtheidealbondlengthin≈.Thedefaultunitsfortheforceconstantarekcal/mole/≈2,butthiscanbecontrolledviatheBONDUNITkeyword. BOND-CUBIC[real] SetsthevalueofthecubictermintheTaylorseriesexpansionformofthebond stretching potentialenergy. The real numbermodifier gives the value of thecoefficientas amultiple of the quadratic coefficient. This term multiplied by the bond stretching energy unitconversionfactor,theforceconstant,andthecubeofthedeviationofthebondlengthfromitsidealvaluegivesthecubiccontributiontothebondstretchingenergy.ThedefaultvalueintheabsenceoftheBOND-CUBICkeywordiszero;i.e.,thecubicbondstretchingtermisomitted.


BOND-QUARTIC[real] SetsthevalueofthequartictermintheTaylorseriesexpansionformofthebondstretchingpotentialenergy.Therealnumbermodifiergivesthevalueofthecoefficientasamultiple of the quadratic coefficient. This term multiplied by the bond stretching energy unitconversionfactor,theforceconstant,andtheforthpowerofthedeviationofthebondlengthfromitsideal value gives the quartic contribution to the bond stretching energy. The default value in theabsenceoftheBOND-QUARTICkeywordiszero;i.e.,thequarticbondstretchingtermisomitted. BOND3 [2 integers&2 reals] This keywordprovides the values for a single bond stretchingparameterspecifictoatomsin3-memberedrings.Theintegermodifiersgivetheatomclassnumbersforthetwokindsofatomsinvolvedinthebondwhichistobedefined.Therealnumbermodifiersgivetheforceconstantvalueforthebondandtheidealbondlengthin≈.Thedefaultunitsfortheforce constant are kcal/mole/≈2, but this can be controlled via the BONDUNIT keyword. If anyBOND3 keywords are present, either in themaster force field parameter file or the keyfile, thenTINKERrequiresthatspecialBOND3parametersbegivenforallbondsin3-memberedrings.IntheabsenceofanyBOND3keywords,standardBONDparameterswillbeusedforbondsin3-memberedrings. BOND4 [2 integers&2 reals] This keywordprovides the values for a single bond stretchingparameterspecifictoatomsin4-memberedrings.Theintegermodifiersgivetheatomclassnumbersforthetwokindsofatomsinvolvedinthebondwhichistobedefined.Therealnumbermodifiersgivetheforceconstantvalueforthebondandtheidealbondlengthin≈.Thedefaultunitsfortheforce constant are kcal/mole/≈2, but this can be controlled via the BONDUNIT keyword. If anyBOND4 keywords are present, either in themaster force field parameter file or the keyfile, thenTINKERrequiresthatspecialBOND4parametersbegivenforallbondsin4-memberedrings.IntheabsenceofanyBOND4keywords,standardBONDparameterswillbeusedforbondsin4-memberedrings BOND5 [2 integers&2 reals] This keywordprovides the values for a single bond stretchingparameterspecifictoatomsin5-memberedrings.Theintegermodifiersgivetheatomclassnumbersforthetwokindsofatomsinvolvedinthebondwhichistobedefined.Therealnumbermodifiersgivetheforceconstantvalueforthebondandtheidealbondlengthin≈.Thedefaultunitsfortheforce constant are kcal/mole/≈2, but this can be controlled via the BONDUNIT keyword. If anyBOND5 keywords are present, either in themaster force field parameter file or the keyfile, thenTINKERrequiresthatspecialBOND5parametersbegivenforallbondsin5-memberedrings.IntheabsenceofanyBOND5keywords,standardBONDparameterswillbeusedforbondsin5-memberedrings BONDTERM[NONE/ONLY] Thiskeywordcontrols useof thebondstretchingpotentialenergyterm. In theabsenceofamodifyingoption, thiskeyword turnsonuseof thepotential.TheNONEoption turns off use of this potential energy term. TheONLYoption turns off all potential energytermsexceptforthisone. BONDTYPE[TAYLOR/MORSE/GAUSSIAN] Chooses the functional formof thebondstretchingpotential. The TAYLOR option selects a Taylor series expansion containing terms from harmonicthrough quartic. The MORSE option selects a Morse potential fit to the ideal bond length andstretching forceconstant parameter values. TheGAUSSIANoption usesan invertedGaussianwithamplitudeequaltotheMorsebonddissociationenergyandwidthsettoreproducethevibrationalfrequencyofaharmonicpotential.ThedefaultistousetheTAYLORpotential. BONDUNIT[real]Setsthescalefactorneededtoconverttheenergyvaluecomputedbythebondstretchingpotentialintounitsofkcal/mole.Thecorrectvalueisforcefielddependentandtypically


providedintheheaderofthemasterforcefieldparameterfile.Thedefaultvalueof1.0isused,iftheBONDUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. C-AXIS[real]SetsthevalueoftheC-axislengthforacrystalunitcell,or,equivalently,theZ-axislengthforaperiodicbox.ThelengthvalueinAngstromsislistedafterthekeyword.Ifthekeywordisabsent,theC-axislengthissetequaltotheA-axislength. C-EXPTERM [real] Sets the value of the ``C'' dispersionmultiplier in theBuckinghamvanderWaalsfunction,i.e.,thevalueofCintheformulaEvdw=e{Aexp[-B(Ro/R)]-C(Ro/R)6}. CAPPA[real] Thiskeyword isused toset thenormal terminationcriterion for the linesearchphaseofTINKERoptimizationroutines.Thelinesearchexitssuccessfully iftheratioofthecurrentgradientprojectiononthelinetotheprojectionatthestartofthelinesearchfallsbelowthevalueofCAPPA.Adefaultvalueof0.1isusedintheabsenceoftheCAPPAkeyword. CHARGE[1integer&1real] Thiskeywordprovidesavalueforasingleatomicpartialchargeelectrostaticparameter.Theintegermodifier,ifpositive,givestheatomtypenumberforwhichthechargeparameteristobedefined.Notethatchargeparametersaregivenforatomtypes,notatomclasses. If the integermodifier is negative, then the parameter value to follow applies only to theindividualatomwhoseatomnumberisthenegativeofthemodifier.Therealnumbermodifiergivesthevaluesoftheatomicpartialchargeinelectrons. CHARGETERM[NONE/ONLY] Thiskeywordcontrolsuseofthecharge-chargepotentialenergytermbetweenpairs of atomic partial charges. In theabsence ofamodifying option, this keywordturnsonuseofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. CHG-12-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtocharge-chargeelectrostatic interactionsbetween1-2connectedatoms, i.e.,atomsthataredirectlybonded.Thedefaultvalueof0.0isused, if theCHG-12-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. CHG-13-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtocharge-chargeelectrostaticinteractionsbetween1-3connectedatoms,i.e.,atomsseparatedbytwocovalentbonds. The default value of 0.0 is used, if the CHG-13-SCALE keyword is not given in either theparameterfileorthekeyfile. CHG-14-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtocharge-charge electrostatic interactions between 1-4 connected atoms, i.e., atoms separated by threecovalentbonds.Thedefaultvalueof1.0isused,iftheCHG-14-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. CHG-15-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtocharge-chargeelectrostaticinteractionsbetween1-5connectedatoms,i.e.,atomsseparatedbyfourcovalentbonds. The default value of 1.0 is used, if the CHG-15-SCALE keyword is not given in either theparameterfileorthekeyfile. CHG-CUTOFF[real] Sets thecutoffdistancevalue inAngstroms forcharge-chargeelectrostaticpotentialenergyinteractions.Theenergyforanypairofsitesbeyondthecutoffdistancewillbesettozero.Otherkeywordscanbeusedtoselectasmoothingschemenearthecutoffdistance.Thedefault


cutoffdistanceintheabsenceoftheCHG-CUTOFFkeywordis infinitefornonperiodicsystemsand9.0forperiodicsystems. CHG-TAPER [real] This keyword allowsmodification of the cutoff window for charge-chargeelectrostatic potential energy interactions. It is similar in form and action to theTAPERkeyword,exceptthatitsvalueappliesonlytothecharge-chargepotential.ThedefaultvalueintheabsenceoftheCHG-TAPERkeywordistobeginthecutoffwindowat0.65ofthecorrespondingcutoffdistance. CHGDPLTERM[NONE/ONLY] Thiskeywordcontrolsuseof thecharge-dipolepotentialenergytermbetween atomic partial chargesandbonddipoles. In theabsence of amodifying option, thiskeywordturnsonuseofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. COLLISION[real]SetsthevalueoftherandomcollisionfrequencyusedintheAndersenstochasticcollisiondynamicsthermostat.Thesuppliedvaluehasunitsoffs-1atom-1andismultipliedinternaltoTINKERbythetimestepinfsandN-2/3whereNisthenumberofatoms.ThedefaultvalueusedintheabsenceoftheCOLLISIONkeywordis0.1whichisappropriateformanysystemsbutmayneedadjustmenttoachieveadequatetemperaturecontrolwithoutperturbingthedynamics. COMPRESS[real] Setsthevalueofthebulksolvent isothermalcompressibility inAtm-1foruseduring pressure computation and scaling inmolecular dynamics computations. The default valueusedintheabsenceoftheCOMPRESSkeywordis0.000046,appropriateforwater.Thisparameterserves as a scale factor for the Groningen-style pressure bath coupling time, and its exact valueshouldnotbeofcriticalimportance. CUTOFF[real]Setsthecutoffdistancevalueforallnonbondedpotentialenergyinteractions.Theenergyforanyofthenonbondedpotentialsofapairofsitesbeyondthecutoffdistancewillbesettozero.Otherkeywordscanbeusedtoselectasmoothingschemenearthecutoffdistance,ortoapplydifferentcutoffdistancestovariousnonbondedenergyterms. DEBUGTurnsonprintingofdetailedinformationandintermediatevaluesthroughouttheprogressofaTINKERcomputation;not recommended forusewith largestructuresor fullpotentialenergyfunctionssinceasummaryofeveryindividualinteractionwillusuallybeoutput. DEFORM[real]Setstheamountofdiffusionequation-stylesmoothingthatwillbeappliedtothepotentialenergysurfacewhenusingtheSMOOTHforcefield.Therealnumberoptionisequivalenttothe``time''valueintheoriginalPiela,etal.formalism;thelargerthevalue,thegreaterthesmoothing.Thedefaultvalueiszero,meaningthatnosmoothingwillbeapplied. DEGREES-FREEDOM[integer] Thiskeywordallowsmanualsettingofthenumberofdegreesoffreedomduringadynamicscalculation.Theintegermodifierisusedbythermostatingmethodsandinotherplacesasthenumberofdegreesoffreedom,overridingthevaluedeterminedbytheTINKERcodeatdynamicsstartup.Intheabsenceofthekeyword,theprogramswillautomaticallycomputethecorrectvaluebasedonthenumberofatomsactiveduringdynamics,bondorotherconstrains,anduseofperiodicboundaryconditions. DELTA-HALGREN [real] Sets the value of the d parameter in Halgren's buffered 14-7 vdwpotentialenergyfunctionalform.IntheabsenceoftheDELTA-HALGRENkeyword,adefaultvalueof0.07isused.


DIELECTRIC [real] Sets thevalueof thebulkdielectric constantused todampallelectrostaticinteractionenergiesforanyoftheTINKERelectrostaticpotentialfunctions.Thedefaultvalueisforcefielddependent,butisusuallyequalto1.0(forAllinger'sMMforcefieldsthedefaultis1.5). DIFFUSE-CHARGE[real]ThiskeywordisusedduringpotentialfunctionsmoothingprocedurestospecifytheeffectivediffusioncoefficienttobeappliedtothesmoothedformoftheCoulomb'sLawcharge-chargepotentialfunction.IntheabsenceoftheDIFFUSE-CHARGEkeyword,adefaultvalueof3.5isused. DIFFUSE-TORSION[real]Thiskeywordisusedduringpotentialfunctionsmoothingprocedurestospecifytheeffectivediffusioncoefficienttobeappliedtothesmoothedformofthetorsionanglepotential function. In the absence of theDIFFUSE-TORSIONkeyword, a default value of 0.0225 isused. DIFFUSE-VDW[real] Thiskeyword isusedduringpotential functionsmoothingprocedures tospecify theeffectivediffusioncoefficient tobeapplied to thesmoothedGaussianapproximation totheLennard-JonesvanderWaalspotentialfunction.IntheabsenceoftheDIFFUSE-VDWkeyword,adefaultvalueof1.0isused. DIGITS[integer] Thiskeywordcontrolsthenumberofdigitsofprecision outputbyTINKERinreportingpotentialenergiesandatomiccoordinates.Theallowedvaluesfortheintegermodifierare4,6and8.Inputvalueslessthan4willbesetto4,andthosegreaterthan8willbesetto8.FinalenergyvaluesreportedbymostTINKERprogramswillcontainthespecifiednumberofdigitstotheright of the decimal point. The number of decimal places to be output for atomic coordinates isgenerallytwolargerthanthevalueofDIGITS.IntheabsenceoftheDIGITSkeywordadefaultvalueof4isused,andenergieswillbereportedto4decimalplaceswithcoordinatesto6decimalplaces. DIPOLE [2 integers & 2 reals] This keyword provides the values for a single bond dipoleelectrostaticparameter.Theintegermodifiersgivetheatomtypenumbersforthetwokindsofatomsinvolvedinthebonddipolewhichistobedefined.TherealnumbermodifiersgivethevalueofthebonddipoleinDebyesandthepositionofthedipolesitealongthebond.Ifthebonddipolevalueispositive,thenthefirstofthetwoatomtypesisthepositiveendofthedipole.Foranegativebonddipolevalue,thefirstatomtypelistedisnegative.Thepositionalongthebondisanoptionalmodifierthatgivesthepostionofthedipolesiteasafractionbetweenthefirstatomtype(position=0)andthesecondatomtype(position=1).Thedefaultforthedipolepositionintheabsenceofaspecifiedvalueis0.5,placingthedipoleatthemidpointofthebond. DIPOLE3 [2 integers & 2 reals] This keyword provides the values for a single bond dipoleelectrostaticparameterspecifictoatomsin3-memberedrings.Theintegermodifiersgivetheatomtypenumbersforthetwokindsofatomsinvolvedinthebonddipolewhichistobedefined.TherealnumbermodifiersgivethevalueofthebonddipoleinDebyesandthepositionofthedipolesitealongthebond.Thedefault for thedipoleposition in theabsenceofa specifiedvalue is0.5,placing thedipoleatthemidpointofthebond.IfanyDIPOLE3keywordsarepresent,eitherinthemasterforcefieldparameterfileorthekeyfile,thenTINKERrequiresthatspecialDIPOLE3parametersbegivenforallbonddipolesin3-memberedrings.IntheabsenceofanyDIPOLE3keywords,standardDIPOLEparameterswillbeusedforbondsin3-memberedrings. DIPOLE4 [2 integers & 2 reals] This keyword provides the values for a single bond dipoleelectrostaticparameterspecifictoatomsin4-memberedrings.Theintegermodifiersgivetheatomtypenumbersforthetwokindsofatomsinvolvedinthebonddipolewhichistobedefined.TherealnumbermodifiersgivethevalueofthebonddipoleinDebyesandthepositionofthedipolesitealongthebond.Thedefault for thedipoleposition in theabsenceofa specifiedvalue is0.5,placing the


dipoleatthemidpointofthebond.IfanyDIPOLE4keywordsarepresent,eitherinthemasterforcefieldparameterfileorthekeyfile,thenTINKERrequiresthatspecialDIPOLE4parametersbegivenforallbonddipolesin4-memberedrings.IntheabsenceofanyDIPOLE4keywords,standardDIPOLEparameterswillbeusedforbondsin4-memberedrings. DIPOLE5 [2 integers & 2 reals] This keyword provides the values for a single bond dipoleelectrostaticparameterspecifictoatomsin5-memberedrings.Theintegermodifiersgivetheatomtypenumbersforthetwokindsofatomsinvolvedinthebonddipolewhichistobedefined.TherealnumbermodifiersgivethevalueofthebonddipoleinDebyesandthepositionofthedipolesitealongthebond.Thedefault for thedipoleposition in theabsenceofa specifiedvalue is0.5,placing thedipoleatthemidpointofthebond.IfanyDIPOLE5keywordsarepresent,eitherinthemasterforcefieldparameterfileorthekeyfile, thenTINKERrequiresthatspecialDIPOLE5parametersbegivenforallbonddipolesin5-memberedrings.IntheabsenceofanyDIPOLE5keywords,standardDIPOLEparameterswillbeusedforbondsin5-memberedrings. DIPOLETERM [NONE/ONLY] This keyword controls use of the dipole-dipole potential energytermbetweenpairsofbonddipoles.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. DIRECT-11-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtothepermanent (direct) field due to atoms within a polarization group during an induced dipolecalculation, i.e., atoms that are in the same polarization group as the atom being polarized. Thedefaultvalueof0.0isused,iftheDIRECT-11-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. DIRECT-12-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtothepermanent (direct) field due to atoms in 1-2 polarization groups during an induced dipolecalculation,i.e.,atomsthatareinpolarizationgroupsdirectlyconnectedtothegroupcontainingtheatombeingpolarized.Thedefaultvalueof0.0isused,iftheDIRECT-12-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. DIRECT-13-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtothepermanent (direct) field due to atoms in 1-3 polarization groups during an induced dipolecalculation, i.e., atoms that are in polarization groups separated by one group from the groupcontaining the atom being polarized. The default value of 0.0 is used, if the DIRECT-13-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. DIRECT-14-SCALE[real]Thiskeywordprovidesamultiplicativescalefactorthatisappliedtothepermanent (direct) field due to atoms in 1-4 polarization groups during an induced dipolecalculation, i.e., atoms that are in polarization groups separated by two groups from the groupcontaining the atom being polarized. The default value of 1.0 is used, if the DIRECT-14-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. DIVERGE[real]ThiskeywordisusedbytheSADDLEprogramtosetthemaximumallowedvalueoftheratioofthegradient lengthalongthepathtothetotalgradientnormattheendofacycleofminimizationperpendiculartothepath.IfthevalueprovidedbytheDIVERGEkeywordisexceeded,thenanothercycleofmaximizationalongthepathisrequired.Adefaultvalueof0.005isusedintheabsenceoftheDIVERGEkeyword. DPL-CUTOFF [real] Sets the cutoff distance value in Angstroms for bond dipole-bond dipoleelectrostaticpotentialenergyinteractions.Theenergyforanypairofbonddipolesitesbeyondthe


cutoffdistancewillbesettozero.Otherkeywordscanbeusedtoselectasmoothingschemenearthecutoffdistance.ThedefaultcutoffdistanceintheabsenceoftheDPL-CUTOFFkeywordisessentiallyinfinitefornonperiodicsystemsand10.0forperiodicsystems. DPL-TAPER[real]Thiskeywordallowsmodificationofthecutoffwindowsforbonddipole-bonddipole electrostatic potential energy interactions. It is similar in form and action to the TAPERkeyword,exceptthatitsvalueappliesonlytothevdwpotential.ThedefaultvalueintheabsenceoftheDPL-TAPERkeywordistobeginthecutoffwindowat0.75ofthedipolecutoffdistance. ECHO[textstring]Thepresenceofthiskeywordcauseswhatevertextfollowsitonthelinetobecopied directly to the output file. This keyword is also active in parameter files. It has no defaultvalue;ifnotextfollowstheECHOkeyword,ablanklineisplacedintheoutputfile. ELECTNEG[3integers&1real]Thiskeywordprovidesthevaluesforasingleelectronegativitybondlengthcorrectionparameter.Thefirsttwointegermodifiersgivetheatomclassnumbersoftheatoms involved in the bond to be corrected. The third integer modifier is the atom class of anelectronegativeatom.Inthecaseofaprimarycorrection,anatomofthisthirdclassmustbedirectlybondedtoanatomofthesecondatomclass.Forasecondarycorrection,thethirdclassisoneatomremovedfromanatomofthesecondclass.Therealnumbermodifieristhevaluein≈bywhichtheoriginalidealbondlengthistobecorrected. ENFORCE-CHIRALITYThiskeywordcausesthechiralityfoundatchiraltetravalentcentersintheinputstructuretobemaintainedduringTINKERcalculations.Thetestforchiralityisnotexhaustive;twoidenticalmonovalentatomsconnectedtoacentercauseittobemarkedasnon-chiral,butlargeequivalentsubstituentsarenotdetected.Trivalent``chiral''centers,forexamplethealphacarboninunited-atomproteinstructures,arenotenforcedaschiral. EPSILONRULE [GEOMETRIC/ARITHMETIC/HARMONIC/HHG] This keyword selects thecombiningruleusedtoderivetheevalueforvanderWaalsinteractions.ThedefaultintheabsenceoftheEPSILONRULEkeywordistousetheGEOMETRICmeanoftheindividualevaluesofthetwoatomsinvolvedinthevanderWaalsinteraction. EWALD ThiskeywordturnsontheuseofEwaldsummationduringcomputationofelectrostaticinteractions in periodic systems. In the current version of TINKER, regular Ewald is used forpolarizable atomicmultipoles, and smooth particle mesh Ewald (PME) is used for charge-chargeinteractions.Ewaldsummationisnotavailableforinteractionsinvolvingbond-centereddipoles.Bydefault, in the absence of the EWALD keyword, distance-based cutoffs are used for electrostaticinteractions. EWALD-ALPHA [real] Sets the value of theEwald coefficientwhich controls thewidth of theGaussianscreeningchargesduringparticlemeshEwaldsummation.IntheabsenceoftheEWALD-ALPHA keyword, a value is chosenwhich causes interactions outside the real-space cutoff to bebelowa fixed tolerance.Formost standardapplicationsofEwaldsummation, theprogramdefaultshouldbeused. EWALD-BOUNDARYThiskeywordinvokestheuseofinsulating(ie,vacuum)boundaryconditionsduringEwald summation, corresponding to themediasurrounding the systemhaving a dielectricvalueof1.Thedefault intheabsenceoftheEWALD-BOUNDARYkeywordistouseconducting(ie,tinfoil)boundaryconditionswherethesurroundingmediaisassumedtohaveaninfinitedielectricvalue.


EWALD-CUTOFF[real]SetsthevalueinAngstromsofthereal-spacedistancecutoffforuseduringEwaldsummation.Bydefault,intheabsenceoftheEWALD-CUTOFFkeyword,avalueof9.0isused. EXIT-PAUSEThiskeywordcausesTINKERprogramstopauseandwaitforacarriagereturnattheend of executation prior to returning control to the operating system. This is useful to keep theexecutionwindow open following termination onmachines runningMicrosoftWindows or AppleMacOS.ThedefaultintheabsenceoftheEXIT-PAUSEkeyword,istoreturncontroltotheoperatingsystemimmediatelyatprogramtermination. EXTRATERM[NONE/ONLY]Thiskeywordcontrolsuseoftheuserdefinedextrapotentialenergyterm. In theabsenceofamodifyingoption, thiskeyword turnsonuseof thepotential.TheNONEoption turns off use of this potential energy term. TheONLYoption turns off all potential energytermsexceptforthisone. FCTMIN[real]ThiskeywordsetsaconvergencecriterionforsuccessfulcompletionofaTINKERoptimization.Ifthevalueoftheoptimizationobjectivefunction,typicallythepotentialenergy, fallsbelow the value set by FCTMIN, then the optimization is deemed to have converged. The defaultvalue in theabsence of theFCTMINkeyword is -1000000, effectively removing this criterion asapossibleagentfortermination. FORCEFIELD[name]Thiskeywordprovidesanamefortheforcefieldtobeusedinthecurrentcalculation.Itsvalueisusuallysetinthemasterforcefieldparameterfileforthecalculation(seethePARAMETERSkeyword)insteadofinthekeyfile. FRICTION[real]Setsthevalueofthefrictionalcoefficientinps-1forusewithstochasticdynamics.The default value used in the absence of the FRICTION keyword is 91.0, which is generallyappropriateforwater. FRICTION-SCALING Thiskeyword turnson theuseofatomicsurfacearea-basedscalingof thefrictional coefficient during stochastic dynamics. When in use, the coefficient for each atom ismultipliedbythatatom'sfractionofexposedsurfacearea.Thedefaultintheabsenceofthekeywordistoomitthescalingandusethefullcoefficientvalueforeachatom. GAMMA[real]Setsthevalueofthegangleofacrystalunitcell,i.e.,theanglebetweenthea-axisandb-axisofaunitcell,or,equivalently,theanglebetweentheX-axisandY-axisofaperiodicbox.ThedefaultvalueintheabsenceoftheGAMMAkeywordistosetthegangleequaltotheaangleasgivenbythekeywordALPHA. GAMMA-HALGREN [real] Sets the value of the g parameter in Halgren's buffered 14-7 vdwpotentialenergyfunctionalform.IntheabsenceoftheDELTA-HALGRENkeyword,adefaultvalueof0.12isused. GAMMAMIN[real]SetstheconvergencetargetvalueforgduringsearchesformaximaalongthequadraticsynchronoustransitusedbytheSADDLEprogram.Thevalueofgisthesquareoftheratioofthegradientprojectionalongthepathtothetotalgradient.Adefaultvalueof0.00001isusedintheabsenceoftheGAMMAMINkeyword. GAUSSTYPE[LJ-2/LJ-4/MM2-2/MM3-2/IN-PLACE] ThiskeywordspecifiestheunderlyingvdwformthataGaussianvdwapproximationwillattempttofit.numberoftermstobeusedinaGaussianapproximationoftheLennard-JonesvanderWaalspotential.Thetextmodifiergivesthenameofthefunctionalformtobeused.ThusLJ-2asamodifierwillresultina2-GaussianfittoaLennard-Jones


vdwpotential.TheGAUSSTYPEkeywordonlytakeseffectwhenVDWTYPEissettoGAUSSIAN.Thiskeywordhasnodefaultvalue. GROUP[integer,integerlist]Thiskeyworddefinesanatomgroupasasubstructurewithinthefullinputmolecularstructure.Thevalueofthefirstintegeristhegroupnumberwhichmustbeintherangefrom1tothemaximumnumberofallowedgroups.Theremainingintergersgivetheatomoratomscontainedinthisgroupasoneormoreatomnumbersorranges.Multiplekeywordlinescanbeusedtospecifyadditionalatomsinthesamegroup.Notethatanatomcanonlybeinonegroup,thelastgrouptowhichitisassignedistheoneused. GROUP-INTERThiskeywordassignsavalueof1.0toallinter-groupinteractionsandavalueof0.0to all intra-group interactions. For example, combination with the GROUP-MOLECULE keywordprovidesforrigid-bodycalculations. GROUP-INTRA Thiskeywordassignsavalueof1.0toallintra-groupinteractionsandavalueof0.0toallinter-groupinteractions. GROUP-MOLECULE Thiskeywordsetseachindividualmolecule in thesystemtobea separateatomgroup,butdoesnotassignweightstogroup-groupinteractions. GROUP-SELECT[2integers,real]Thiskeywordgivestheweightinthefinalpotentialenergyofaspecifiedsetofintra-orintergroupinteractions.Theintegermodifiersgivethegroupnumbersofthegroupsinvolved.Ifthetwonumbersarethesame,thenanintragroupsetofinteractionsisspecified.Therealmodifiergivestheweightbywhichallenergetic interactionsinthissetwillbemultipliedbeforeincorporationintothefinalpotentialenergy.Ifomittedasakeywordmodifier,theweightwillbesetto1.0bydefault.IfanySELECT-GROUPkeywordsarepresent,thenanysetofinteractionsnotspecifiedinaSELECT-GROUPkeywordisgivenazeroweight.ThedefaultwhennoSELECT-GROUPkeywords are specified is to use all intergroup interactions with a weight of 1.0 and to set allintragroupinteractionstozero. HBOND[2integers&2reals] ThiskeywordprovidesthevaluesfortheMM3-styledirectionalhydrogenbondingparametersforasinglepairofatoms.Theintegermodifiersgivethepairofatomclass numbers for which hydrogen bonding parameters are to be defined. The two real numbermodifiers give the values of theminimumenergy contact distance in ≈ and thewell depth at theminimumdistanceinkcal/mole. HESS-CUTOFF[real]ThiskeyworddefinesalowerlimitforsignificantHessianmatrixelements.Duringcomputationof theHessianmatrixofpartial secondderivatives,anymatrixelementswithabsolutevaluebelowHESS-CUTOFFwillbesettozeroandomittedfromthesparsematrixHessianstorageschemeusedbyTINKER.Formostcalculations,thedefaultintheabsenceofthiskeywordiszero, i.e.,all elementswillbestored.FormostTruncatedNewtonoptimizations theHessiancutoffwillbechosendynamicallybytheoptimizer. HGUESS[real] SetsaninitialguessfortheaveragevalueofthediagonalelementsofthescaledinverseHessianmatrix used by the optimally conditioned variablemetric optimization routine. Adefaultvalueof0.4isusedintheabsenceoftheHGUESSkeyword. IMPROPER[4integers&2reals]ThiskeywordprovidesthevaluesforasingleCHARMM-styleimproperdihedralangleparameter.


IMPROPTERM[NONE/ONLY]ThiskeywordcontrolsuseoftheCHARMM-styleimproperdihedralanglepotentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. IMPROPUNIT[real] Sets thescale factorneeded toconvert theenergyvaluecomputedby theCHARMM-styleimproperdihedralanglepotentialintounitsofkcal/mole.Thecorrectvalueisforcefield dependentand typically provided in the header of themaster force field parameter file. Thedefaultvalueof1.0isused,iftheIMPROPUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. IMPTORS[4integers&upto3real/real/integertriples]ThiskeywordprovidesthevaluesforasingleAMBER-styleimpropertorsionalangleparameter.Thefirst fourintegermodifiersgivetheatom class numbers for the atoms involved in the improper torsional angle to be defined. Byconvention, the thirdatomclassof the four is the trigonalatomonwhich the improper torsion iscentered.Thetorsionalanglecomputedisliterallythatdefinedbythefouratomclassesintheorderspecifiedbythekeyword.Eachoftheremainingtriplesofreal/real/integermodifiersgivethehalf-amplitude, phase offset in degrees and periodicity of a particular improper torsional term,respectively.Periodicitiesthrough3-foldareallowedforimpropertorsionalparameters. IMPTORSTERM[NONE/ONLY]ThiskeywordcontrolsuseoftheAMBER-styleimpropertorsionalanglepotentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. IMPTORSUNIT[real] SetsthescalefactorneededtoconverttheenergyvaluecomputedbytheAMBER-styleimproper torsionalanglepotential intounitsofkcal/mole.Thecorrectvalue isforcefield dependentand typically provided in the header of themaster force field parameter file. Thedefaultvalueof1.0isused,iftheIMPTORSUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. INACTIVE[integerlist] Setsthelistof inactiveatomsduringaTINKERcomputation.Individualpotential energy terms are not computed when all atoms involved in the term are inactive. ForCartesian space calculations, inactive atoms are not allowed to move. For torsional spacecalculations, rotationsarenotallowedwhen thereare inactiveatomsonbothsidesof the rotatedbond.Multiple INACTIVE linescanbepresent in thekeyfile, andoneach line thekeywordcanbefollowedbyoneormoreatomnumbersorranges.IfanyINACTIVEkeysarefound,allatomsaresetto active except those listed on the INACTIVE lines. TheACTIVE keyword overrides all INACTIVEkeywordsfoundinthekeyfile. INTEGRATE[VERLET/BEEMAN/STOCHASTIC/RIGIDBODY]Choosestheintegrationmethodforpropagationofdynamicstrajectories.Thekeywordisfollowedonthesamelinebythenameoftheoption.StandardNewtonianMDcanberunusingeitherVERLETfortheVelocityVerletmethod,orBEEMANforthevelocityformofBernieBrook's ``BetterBeeman''method.AVelocityVerlet-basedstochastic dynamics trajectory is selected by the STOCHASTIC modifier. A rigid-body dynamicsmethod is selected by the RIGIDBODYmodifier. The default integration scheme is MD using theBEEMANmethod. INTMAX[integer]Setsthemaximumnumberofinterpolationcyclesthatwillbeallowedduringthe line search phase of an optimization. All gradient-based TINKER optimization routines use acommonlinesearchroutineinvolvingquadraticextrapolationandcubicinterpolation.IfthevalueofINTMAXisreached,anerrorstatusissetforthelinesearchandthesearchisrepeatedwithamuch


smaller initial step size. The default value in the absence of this keyword is optimization routinedependent,butisusuallyintherange5to10. LAMBDA[real]Thiskeywordsetsthevalueofthelpathparameterforfreeenergyperturbationcalculations.Therealnumbermodifierspecifiesthepositionalongthemutationpathandmustbeanumberintherangefrom0(initialstate)to1(finalstate).TheactualatomsinvolvedinthemutationaregivenseparatelyinindividualMUTATEkeywordlines. LBFGS-VECTORS[integer]Setsthenumberofcorrectionvectorsusedbythelimited-memoryL-BFGSoptimizationroutine.Thecurrentmaximumallowablevalue,andthedefaultintheabsenceoftheLBFGS-VECTORSkeywordis15. LIGHTS This keyword turns on Method of Lights neighbor generation for the partial chargeelectrostatics and any of the van derWaals potentials. Thismethodwill yield identical energeticresults to thestandarddouble loopmethod.MethodofLightswillbe fasterwhen thevolumeofaspherewithradiusequaltothenonbondcutoffdistanceissignificantlylessthanhalfthevolumeofthetotalsystem(i.e.,thefullmolecularsystem,thecrystalunitcellortheperiodicbox).Itrequireslessstoragethanpairwiseneighborlists. LIST-BUFFER[real]SetsthesizeoftheneighborlistbufferinAngstroms.Thisvalueisaddedtotheactualcutoffdistancetodeterminewhichpairswillbekeptontheneighborlist.Thesamebuffervalueisusedforallneighborlists.Thedefaultvalueintheabsenceof2.0isusedintheabsenceoftheLIST-BUFFERkeyword. MAXITER[integer]SetsthemaximumnumberofminimizationiterationsthatwillbeallowedforanyTINKERprogramthatusesanyofthenonlinearoptimizationroutines.Thedefaultvalueintheabsenceofthiskeywordisprogramdependent,butisalwayssettoaverylargenumber. METALThiskeywordprovidesthevaluesforasingletransitionmetalligandfieldparameter.Notethiskeywordispresentinthecode,butnotactiveinthecurrentversionofTINKER. METALTERM [NONE/ONLY] This keyword controls use of the transition metal ligand fieldpotential energy term. In the absence of a modifying option, this keyword turns on use of thepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. MM2-STRBNDThiskeywordswitchesthebehaviorofthestretch-bendpotentialfunctiontomatchthe formulation used by the MM2 force field. In MM2, stretching of bonds to attached hydrogenatomsisnotincludingincomputingthestretch-bendcrosstermenergy.Thedefaultbehaviorintheabsence of thiskeyword is to include stretching of attachedhydrogen atoms as in theMM3 forcefield. MPOLE-12-SCALE [real] This keywordprovidesamultiplicative scale factor that isapplied topermanentatomicmultipoleelectrostaticinteractionsbetween1-2connectedatoms,i.e.,atomsthataredirectlybonded.Thedefaultvalueof0.0isused,iftheMPOLE-12-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. MPOLE-13-SCALE [real] This keywordprovidesamultiplicative scale factor that isapplied topermanent atomic multipole electrostatic interactions between 1-3 connected atoms, i.e., atomsseparatedbytwocovalentbonds.Thedefaultvalueof0.0isused,iftheMPOLE-13-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile.


MPOLE-14-SCALE [real] This keywordprovidesamultiplicative scale factor that isapplied topermanent atomic multipole electrostatic interactions between 1-4 connected atoms, i.e., atomsseparatedbythreecovalentbonds.Thedefaultvalueof1.0isused,iftheMPOLE-14-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. MPOLE-15-SCALE [real] This keywordprovidesamultiplicative scale factor that isapplied topermanent atomic multipole electrostatic interactions between 1-5 connected atoms, i.e., atomsseparatedbyfourcovalentbonds.Thedefaultvalueof1.0isused,iftheMPOLE-15-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. MPOLE-CUTOFF[real]SetsthecutoffdistancevalueinAngstromsforatomicmultipolepotentialenergyinteractions.Theenergyforanypairofsitesbeyondthecutoffdistancewillbesettozero.Otherkeywordscanbeusedtoselectasmoothingschemenearthecutoffdistance.ThedefaultcutoffdistanceintheabsenceoftheMPOLE-CUTOFFkeywordis infinitefornonperiodicsystemsand9.0forperiodicsystems. MPOLE-TAPER[real]Thiskeywordallowsmodificationofthecutoffwindowforatomicmultipolepotentialenergyinteractions.ItissimilarinformandactiontotheTAPERkeyword,exceptthatitsvalueappliesonlytotheatomicmultipolepotential.ThedefaultvalueintheabsenceoftheMPOLE-TAPERkeywordistobeginthecutoffwindowat0.65ofthecorrespondingcutoffdistance. MPOLETERM [NONE/ONLY] This keyword controls use of the atomicmultipoleelectrostaticspotential energy term. In the absence of a modifying option, this keyword turns on use of thepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. MULTIPOLE [5 lineswith: 3 or4 integers&1 real; 3 reals; 1 real; 2 reals; 3 reals] Thiskeywordprovides thevalues fora setofatomicmultipoleparametersata single site.Acompletekeywordentryconsistsofthreeconsequtivelines,thefirstlinecontainingtheMULTIPOLEkeywordand the two following lines. The first line contains three integerswhich define the atom type onwhichthemultipolesarecentered,andtheZ-axisandX-axisdefiningatomtypesforthiscenter.TheoptionalfourthintegercontainstheY-axisdefiningatomtype,andisonlyrequiredforlocallychiralmultipole sites.Therealnumberon the first linegivesthemonopole (atomiccharge)inelectrons.ThesecondlinecontainsthreerealnumberswhichgivetheX-,Y-andZ-componentsoftheatomicdipole in electron-≈. The final three lines, consisting of one, two and three real numbers give theuppertriangleofthetracelessatomicquadrupoletensorinelectron-≈2. MUTATE[3integers] Thiskeywordisusedtospecifyatomstobemutatedduringfreeenergyperturbationcalculations.Thefirstintegermodifiergivestheatomnumberofanatominthecurrentsystem.Thefinaltwomodifiervaluesgivetheatomtypescorrespondingthethel=0andl=1statesofthespecifiedatom. MUTUAL-11-SCALE[real] Thiskeywordprovidesamultiplicativescalefactorthat isappliedtothe induced (mutual) field due to atoms within a polarization group during an induced dipolecalculation, i.e., atoms that are in the same polarization group as the atom being polarized. Thedefaultvalueof1.0isused, if theMUTUAL-11-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. MUTUAL-12-SCALE[real] Thiskeywordprovidesamultiplicativescalefactorthat isappliedtothe induced (mutual) field due to atoms in 1-2 polarization groups during an induced dipole


calculation,i.e.,atomsthatareinpolarizationgroupsdirectlyconnectedtothegroupcontainingtheatombeingpolarized.Thedefaultvalueof1.0isused,iftheMUTUAL-12-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. MUTUAL-13-SCALE[real] Thiskeywordprovidesamultiplicativescalefactorthat isappliedtothe induced (mutual) field due to atoms in 1-3 polarization groups during an induced dipolecalculation, i.e., atoms that are in polarization groups separated by one group from the groupcontaining the atom being polarized. The default value of 1.0 is used, if the MUTUAL-13-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. MUTUAL-14-SCALE[real] Thiskeywordprovidesamultiplicativescalefactorthat isappliedtothe induced (mutual) field due to atoms in 1-4 polarization groups during an induced dipolecalculation, i.e., atoms that are in polarization groups separated by two groups from the groupcontaining the atom being polarized. The default value of 1.0 is used, if the MUTUAL-14-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. NEIGHBOR-GROUPS This keyword causes the attached atom to be used in determining thecharge-chargeneighbordistanceforallmonovalentatomsinthemolecularsystem.Itsusecausesallmonovalentatomstobetreatedthesameastheirattachedatomsforpurposesofincludingorscaling1-2, 1-3 and 1-4 interactions. This option works only for the simple charge-charge electrostaticpotential; it does not affect bond dipole or atomic multipole potentials. The NEIGHBOR-GROUPSschemeissimilartothatusedbysomecommonforcefieldssuchasENCAD. NEIGHBOR-LIST Thiskeywordturnsonpairwiseneighborlistsforpartialchargeelectrostatics,polarizemultipole electrostatics and any of the van derWaals potentials. Thismethodwill yieldidenticalenergeticresultstothestandarddoubleloopmethod. NEUTRAL-GROUPSThiskeywordcausestheattachedatomtobeusedindeterminingthecharge-chargeinteractioncutoffdistanceforallmonovalentatomsinthemolecularsystem.Itsusereducescutoffdiscontinuitiesbyavoidingsplittingmanyof the largest chargeseparations found in typicalmolecules.Note that this keyworddoes not rigorously implement the usual concept ofa ``neutralgroup''asusedintheliteraturewithAMBER/OPLSandotherforcefields.Thisoptionworksonlyforthesimplecharge-chargeelectrostaticpotential; itdoesnotaffectbonddipoleoratomicmultipolepotentials. NEWHESS [integer] Sets the number of algorithmic iterations between recomputation of theHessianmatrix. At present this keyword applies exclusively to optimizations using the TruncatedNewtonmethod.Thedefaultvalueintheabsenceofthiskeywordis1,i.e.,theHessianiscomputedoneveryiteration. NEXTITER [integer] Sets the iterationnumber to be used for the first iteration of thecurrentcomputation. At present this keyword applies to optimization procedureswhere its usecaneffectconvergencecriteria,timingofrestarts,andsoforth.Thedefaultintheabsenceofthiskeywordistotaketheinitialiterationasiteration1. NOSE-MASS[real] ThiskeywordsetsthemassofparticlesmakinguptheNose-Hooverchaininthatthermostatingmethod.ThedefaultintheabsenceoftheNOSE-MASSkeywordistouseamassof0.1. NOVERSIONTurnsofftheuseofversionnumbersappendedtotheendoffilenamesasthemethodforgeneratingfilenamesforupdatedcopiesofanexistingfile.Thepresenceofthiskeywordresultsindirectuseofinputfilenameswithoutasearchforthehighestavailableversion,andrequiresthe


entry of specific output file names in many additional cases. By default, in the absence of thiskeyword, TINKER generates and attaches version numbers in a manner similar to the DigitalOpenVMS operating system. For example, subsequent new versions of the file molecule.xyzwouldbewrittenfirsttothefile molecule.xyz_2,thentomolecule.xyz_3,etc. OCTAHEDRONSpecifiesthattheperiodic``box''isatruncatedoctahedronwithmaximaldistanceacrossthetruncatedoctahedronasgivenbytheA-AXISkeyword.Allotherunitcellandperiodicboxsize-definingkeywordsareignorediftheOCTAHEDRONkeywordispresent. OPBEND[2integers&1real] ThiskeywordprovidesthevaluesforasingleAllingerMM-styleout-of-planeanglebendingpotentialparameter.The first integermodifier is theatomclassof thecentral trigonal atom and the second integer is the atom class of the out-of-plane atom. The realnumbermodifiergivestheforceconstantvaluefortheout-of-planeangle.Thedefaultunitsfortheforceconstantarekcal/mole/radian2,butthiscanbecontrolledviatheOPBENDUNITkeyword. OPBENDTERM[NONE/ONLY] Thiskeywordcontrolsuseof theAllingerMM-styleout-of-planebendingpotentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. OPBENDUNIT[real] Sets thescale factorneeded toconvert theenergyvaluecomputedby theAllingerMM-styleout-of-planebendingpotential intounitsofkcal/mole.Thecorrectvalueisforcefield dependentand typically provided in the header of themaster force field parameter file. Thedefaultof(p/180)2=0.0003046isused,iftheOPBENDUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. OPDIST[4integers&1real]Thiskeywordprovidesthevaluesforasingleout-of-planedistancepotentialparameter.Thefirstintegermodifieristheatomclassofthecentraltrigonalatomandthethreefollowingintegermodifiersaretheatomclassesofthethreeattachedatoms.Therealnumbermodifier is the forceconstant for theharmonicfunctionof theout-of-planedistanceof thecentralatom.Thedefaultunits for the forceconstantarekcal/mole/≈2,but this canbecontrolledvia theOPDISTUNITkeyword. OPDISTTERM [NONE/ONLY] This keyword controls use of the out-of-plane distance potentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONE option turns off use of this potential energy term. The ONLY option turns off all potentialenergytermsexceptforthisone. OPDISTUNIT[real]Setsthescalefactorneededtoconverttheenergyvaluecomputedbytheout-of-plane distance potential into units of kcal/mole. The correct value is force field dependent andtypicallyprovidedintheheaderofthemasterforcefieldparameterfile.Thedefaultvalueof1.0isused,iftheOPDISTUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. OVERWRITE Causes TINKER programs, such as minimizations, that output intermediatecoordinate sets to create a single disk file for the intermediate results which is successivelyoverwritten with the new intermediate coordinates as they become available. This keyword isessentiallytheoppositeoftheSAVECYCLEkeyword. PARAMETERS[filename]Providesthenameoftheforcefieldparameterfiletobeusedforthecurrent TINKER calculation. The standard file name extension for parameter files, .prm, is anoptionalpartofthefilenamemodifier.ThedefaultintheabsenceofthePARAMETERSkeywordisto


lookforaparameterfilewiththesamebasenameasthemolecularsystemandendinginthe.prmextension. If a valid parameter file is not found, the user will asked to provide a file nameinteractively. PIATOM[1integer&3reals] ThiskeywordprovidesthevaluesforthepisystemMOpotentialparametersforasingleatomclassbelongingtoapisystem. PIBOND[2integers&2reals]ThiskeywordprovidesthevaluesforthepisystemMOpotentialparametersforasingletypeofpisystembond. PIBOND4[2integers&2reals]ThiskeywordprovidesthevaluesforthepisystemMOpotentialparametersforasingletypeofpisystembondcontainedina4-memberedring. PIBOND5[2integers&2reals]ThiskeywordprovidesthevaluesforthepisystemMOpotentialparametersforasingletypeofpisystembondcontainedina5-memberedring. PISYSTEM [integer list] This keyword sets the atoms within a molecule that are part of aconjugatedp-system.Thekeyword is followedon thesame linebya listofatomnumbersand/oratomrangesthatconstitutethep-system.TheAllingerMMforcefieldsusethisinformationtosetupanMOcalculationusedtoscalebondandtorsionparametersinvolvingp-systematoms. PITORS[2integers&1real] Thiskeywordprovidesthevaluesforasinglepi-orbitaltorsionalangle potential parameter. The two integermodifiers give the atom class numbers for the atomsinvolvedinthecentralbondofthetorsionalangletobeparameterized.Therealmodifiergivesthevalue of the 2-fold Fourier amplitude for the torsional angle between p-orbitals centered on thedefinedbondatomclasses.Thedefaultunitsforthestretch-torsionforceconstantcanbecontrolledviathePITORSUNITkeyword. PITORSTERM[NONE/ONLY]Thiskeywordcontrolsuseofthepi-orbitaltorsionalanglepotentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONE option turns off use of this potential energy term. The ONLY option turns off all potentialenergytermsexceptforthisone. PITORSUNIT[real]Setsthescalefactorneededtoconverttheenergyvaluecomputedbythepi-orbital torsionalanglepotential intounitsofkcal/mole.Thecorrectvalue isforce fielddependentandtypicallyprovidedintheheaderofthemasterforcefieldparameterfile.Thedefaultvalueof1.0isused,ifthePITORSUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. PME-GRID[3integers]ThiskeywordsetsthedimensionsofthechargegridusedduringparticlemeshEwaldsummation.ThethreemodifiersgivethesizealongtheX-,Y-andZ-axes,respectively.IfeithertheY-orZ-axisdimensionsareomitted,thentheyaresetequaltotheX-axisdimension.ThedefaultintheabsenceofthePME-GRIDkeywordistosetthegridsizealongeachaxistothesmallestpowerof2,3and/or5whichisatleastaslargeas1.5timestheaxislengthinAngstoms.NotethattheFFTusedbyPMEisnotrestrictedto,butismostefficientfor,gridsizeswhicharepowersof2,3and/or5. PME-ORDER [integer] This keyword sets the order of the B-spline interpolation used duringparticle mesh Ewald summation. A default value of 8 is used in the absence of the PME-ORDERkeyword.


POLAR-12-SCALE [real] This keywordprovidesamultiplicative scale factor that isapplied topolarization interactions between 1-2 polarization groups, i.e., pairs of atoms that are in directlyconnectedpolarizationgroups.Thedefaultvalueof0.0isused, if thePOLAR-12-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. POLAR-13-SCALE [real] This keywordprovidesamultiplicative scale factor that isapplied topolarizationinteractionsbetween1-3polarizationgroups,i.e.,pairsofatomsthatareinpolarizationgroups separated by one other group. The default value of 0.0 is used, if the POLAR-13-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. POLAR-14-SCALE [real] This keywordprovidesamultiplicative scale factor that isapplied topolarizationinteractionsbetween1-4polarizationgroups,i.e.,pairsofatomsthatareinpolarizationgroups separated by two other groups. The default value of 1.0 is used, if the POLAR-14-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. POLAR-15-SCALE [real] This keywordprovidesamultiplicative scale factor that isapplied topolarizationinteractionsbetween1-5polarizationgroups,i.e.,pairsofatomsthatareinpolarizationgroups separated by three other groups. The default value of 1.0 is used, if the POLAR-15-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. POLAR-DAMP[2reals]Controlsthestrengthofthedampingfunctionappliedtoinduceddipolesand dipole polarization interaction energies. The first modifier sets the radius in Angstoms of ahypothetical atomwith unit polarizability,while the secondmodifier sets the scale factor for theexponentofthe dampingfunction.Thedefaultvaluesfortheradiusandthescalefactorare1.662and1.0,respectively.Dampingiseliminatedentirelybyusingthiskeywordtosettheradiusvaluetozero. POLAR-EPS [real] Thiskeywordsets theconvergencecriterionappliedduringcomputationofself-consistent induceddipoles.Thecalculationisdeemedtohaveconvergedwhenthermschange(inDebyes)of theinduceddipolesatallpolarizablesites is less than thevaluespecifiedwith thiskeyword.Thedefaultvalueintheabsenceofthekeywordis10-6Debyes. POLAR-SOR[real]Setsasuccessiveoverrelaxation(SOR)factorforuseincomputationofinducedatomicdipoles.Optimalvaluesforthiskeywordwillspeedtheinduceddipolecalculation,andpoorvaluescanresultinconvergencefailure.ThedefaultvalueintheabsenceofthePOLAR-SORkeywordis0.7whichoftenareasonablevaluewhenshort-rangeintramolecularpolarizationispresent.Formodelslackingintramolecularpolarization,keywordvaluescloserto1.0maybeoptimal. POLARIZATION [DIRECT/MUTUAL] Selects between the use of direct and mutual dipolepolarizationforforcefieldsthat incorporatethepolarizationterm.TheDIRECTmodifieravoidsaniterativecalculation by using only the permanent electric field in computation of induceddipoles.TheMUTUALoption,whichisthedefaultintheabsenceofthePOLARIZATIONkeyword,iteratestheinduceddipolestoself-consistency. POLARIZE[1integer,1real&upto4integers] Thiskeywordprovidesthevaluesforasingleatomicdipolepolarizabilityparameter.Theintegermodifier,ifpositive,givestheatomtypenumberforwhichapolarizabilityparameteristobedefined.Ifthefirstintegermodifierisnegative,thentheparametervaluetofollowappliesonlytotheindividualatomwhoseatomnumberisthenegativeofthemodifier.Therealnumbermodifiergives thevalueof thedipolepolarizability in≈3.The finalintegermodifierslisttheatomtypenumbersofatomsdirectlybondedtothecurrentatomandwhichwillbeconsideredtobepartofthecurrentatom'spolarizationgroup.


POLARIZETERM [NONE/ONLY] This keyword controls use of the atomic dipole polarizationpotential energy term. In the absence of a modifying option, this keyword turns on use of thepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. POLYMER-CUTOFF [real] Sets the value of an additional cutoff parameter needed for infinitepolymersystems.Thisvaluemustbesetto lessthanhalftheminimalperiodicboxdimensionandshould be greater than the largest possible interatomic distance that can be subject to scaling orexclusion as a local electrostatic or van derWaals interaction. The default in the absence of thePOLYMER-CUTOFFkeywordis5.5Angstroms. PRINTOUT[integer]Ageneralparameterforiterativeproceduressuchasminimizationsthatsetsthenumberof iterationsbetweenwritesof status information to thestandardoutput.Thedefaultvalueintheabsenceofthekeywordis1,i.e.,thecalculationstatusisgiveneveryiteration. RADIUSRULE[ARITHMETIC/GEOMETRIC/CUBIC-MEAN]Setsthefunctionalformoftheradiuscombining rule for heteroatomic van derWaals potential energy interactions. The default in theabsenceoftheRADIUSRULEkeywordistousethearithmeticmeancombiningruletogetradii forheteroatomicinteractions. RADIUSSIZE [RADIUS/DIAMETER] Determineswhether theatomsizevaluesgiven invanderWaalsparametersreadfromVDWkeywordstatementsareinterpretedasatomicradiusordiametervalues.ThedefaultintheabsenceoftheRADIUSSIZEkeywordistoassumethatvdwsizeparametersaregivenasradiusvalues. RADIUSTYPE [R-MIN/SIGMA] Determines whether atom size values given in van derWaalsparametersreadfromVDWkeywordstatementsareinterpretedaspotentialminimum(Rmin)orLJ-stylesigma(s)values.ThedefaultintheabsenceoftheRADIUSTYPEkeywordistoassumethatvdwsizeparametersaregivenasRminvalues. RANDOMSEED[integer]Followedbyanintegervalue,thiskeywordsetstheinitialseedvalueforthe random number generator used by TINKER. Setting RANDOMSEED to the same value as anearlierrunwillallowexactreproductionoftheearliercalculation.(Notethatthiswillnotholdacrossdifferentmachinetypes.)RANDOMSEEDshouldbesettoapositiveintegerlessthanabout2billion.IntheabsenceoftheRANDOMSEEDkeywordtheseedischosen``randomly''baseduponthenumberofsecondsthathaveelapsedinthecurrentdecade. RATTLE [BONDS/ANGLES/DIATOMIC/TRIATOMIC/WATER] Invokes the rattle algorithm, avelocityversionofshake,onportionsofamolecularsystemduringamoleculardynamiccalculation.TheRATTLEkeywordcanbefollowedbyanyofthemodifiersshown,inwhichcasealloccurrencesofthemodifierspeciesareconstrainedatidealvaluestakenfromthebondandangleparametersoftheforcefieldinuse.Intheabsenceofanymodifier,RATTLEconstrainsallbondstohydrogenatomsatidealbondlengths. RATTLE-DISTANCE[2integers] Thiskeywordallowstheuseofa ``Rattle''constraintbetweenthetwoatomswhosenumbersarespecifiedonthekeywordline.Ifthetwoatomsareinvolvedinacovalentbond, then theirdistanceisconstrained to the idealbond length fromtheforce field.Fornonbondedatoms,therattleconstraintisfixedattheirdistanceintheinputcoordinatefile. RATTLE-LINE[integer]Thiskeyword


RATTLE-ORIGIN[integer]Thiskeyword RATTLE-PLANE[integer]Thiskeyword REACTIONFIELD [2 reals & 1 integer] This keyword provides parameters needed for thereaction field potential energycalculation. The two realmodifiersgive the radius of the dielectriccavity and the ratio of the bulk dielectric outside the cavity to that inside the cavity. The integermodifiergivesthenumberoftermsinthereactionfieldsummationtobeused.IntheabsenceoftheREACTIONFIELDkeyword,thedefaultvaluesareacavityofradius1000000≈,adielectricratioof80anduseofonlythefirsttermofthereactionfieldsummation. REDUCE[real] Specifiesthefractionbetweenzeroandonebywhichthepathbetweenstartingandfinalconformationalstatewillbeshortenedateachmajorcycleofthetransitionstate locationalgorithmimplementedbytheSADDLEprogram.Thiscausesthepathendpointstomoveupandoutoftheterminalstructurestowardthetransitionstateregion.Infavorablecases,anonzerovalueoftheREDUCEmodifiercanspeedconvergencetothetransitionstate.ThedefaultvalueintheabsenceoftheREDUCEkeywordiszero. RESTRAIN-ANGLE [3 integers & 3 reals] This keyword implements a flat-welled harmonicpotentialthatcanbeusedtorestraintheanglebetweenthreeatomstoliewithinaspecifiedanglerange. The integermodifiers contain the atom numbers of the three atomswhose angle is to berestrained.Thefirstrealmodifieristheforceconstantinkcal/degree2fortherestraint.Thelasttworealmodifiersgivethelowerandupperboundsindegreesontheallowedanglevalues.Iftheanglelies between the lower andupper bounds, the restraint potential is zero.Outside the bounds, theharmonicrestraintisapplied.Iftheanglerangemodifiersareomitted,thentheatomsarerestrainedtotheanglefoundintheinputstructure.Iftheforceconstantisalsoomitted,adefaultvalueof10.0isused. RESTRAIN-DISTANCE[2integers&3reals] Thiskeywordimplementsaflat-welledharmonicpotentialthatcanbeusedtorestraintwoatomstoliewithinaspecifieddistancerange.Theintegermodifiers contain the atom numbers of the two atoms to be restrained. The first real modifierspecifiestheforceconstantinkcal/≈2fortherestraint.Thenexttworealmodifiersgivethelowerand upper bounds in ≈ngstroms on the allowed distance range. If the interatomic distance liesbetween these lower and upper bounds, the restraint potential is zero. Outside the bounds, theharmonic restraint is applied. If the distance range modifiers are omitted, then the atoms arerestrained to the interatomic distance found in the input structure. If the force constant is alsoomitted,adefaultvalueof100.0isused. RESTRAIN-GROUPS [2 integers&3 reals] This keyword implements a flat-welled harmonicdistancerestraintbetweenthecenters-of-massoftwogroupsofatoms.TheintegermodifiersarethenumbersofthetwogroupswhichmustbedefinedseparatelyviatheGROUPkeyword.Thefirstrealmodifieristheforceconstantinkcal/≈2fortherestraint.Thelasttworealmodifiersgivethelowerand upper bounds in ≈ngstroms on the allowed intergroup center-of-mass distance values. If thedistance rangemodifiers are omitted, then the groupsare restrained to the distance found in theinputstructure.Iftheforceconstantisalsoomitted,adefaultvalueof100.0isused. RESTRAIN-POSITION [1 integer& 5 reals] This keyword provides the ability to restrain anindividual atom to a specified coordinate position. The initial integermodifier contains the atomnumberoftheatomtoberestrained.Thefirstrealmodifiersetstheforceconstantinkcal/≈2fortheharmonicrestraintpotential.ThenextthreerealnumbermodifiersgivetheX-,Y-andZ-coordinates


to which the atom is tethered. The final real modifier defines a sphere around the specifiedcoordinateswithinwhich therestraintvalue is zero. Iftheexclusionsphereradius isomitted, it istakentobezero.Ifthecoordinatesareomitted,thentheatomisrestrainedtotheorigin.Iftheforceconstantisalsoomitted,adefaultvalueof100.0isused. RESTRAIN-TORSION[4 integers&3reals] Thiskeyword implementsa flat-welledharmonicpotentialthatcanbeusedtorestrainthetorsionalanglebetweenfouratomstoliewithinaspecifiedangle range. The initial integer modifiers contains the atom numbers of the four atoms whosetorsionalangle,computedintheatomorderlisted,istoberestrained.Thefirstrealmodifiergivesaforceconstantinkcal/degree2fortherestraint.Thelasttworealmodifiersgivethelowerandupperbounds indegreeson theallowed torsionalanglevalues.Theanglevaluesgivencanwraparoundacross-180and+180degrees.Outsidetheallowedanglerange,theharmonicrestraintisapplied.Iftheanglerangemodifiersareomitted,thentheatomsarerestrainedtothetorsionalanglefoundintheinputstructure.Iftheforceconstantisalsoomitted,adefaultvalueof1.0isused. RESTRAINTERM [NONE/ONLY] This keyword controls use of the restraint potential energyterms.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthesepotentials.TheNONEoptionturnsoffuseofthesepotentialenergyterms.TheONLYoptionturnsoffallpotentialenergytermsexceptfortheseterms. RXNFIELDTERM [NONE/ONLY] This keyword controls use of the reaction field continuumsolvationpotentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. SADDLEPOINT The presence of this keyword allows Newton-style second derivative-basedoptimizationroutineusedbyNEWTON,NEWTROTandotherprogramstoconvergetosaddlepointsaswellasminimaonthepotentialsurface.Bydefault,intheabsenceoftheSADDLEPOINTkeyword,checks are applied that prevent convergence to stationary points having directions of negativecurvature. SAVE-CYCLE This keyword causes TINKER programs, such as minimizations, that outputintermediatecoordinatesets to saveeachsuccessiveset to thenext consecutivelynumberedcyclefile.TheSAVE-CYCLEkeywordistheoppositeoftheOVERWRITEkeyword. SAVE-FORCEThiskeywordcausesTINKERmoleculardynamicscalculationstosavethevaluesofthe force components on eachatom to a separate cycle file. These files arewrittenwhenever theatomic coordinate snapshots are written during the dynamics run. Each atomic force file namecontainsasasuffixthecyclenumberfollowedbytheletterf. SAVE-INDUCED This keyword causes TINKER molecular dynamics calculations that involvepolarizable atomic multipoles to save the values of the induced dipole components on eachpolarizable atom to a separate cycle file. These files arewrittenwhenever the atomic coordinatesnapshotsarewrittenduringthedynamicsrun.Eachinduceddipolefilenamecontainsasasuffixthecyclenumberfollowedbytheletteru. SAVE-VELOCITYThiskeywordcausesTINKERmoleculardynamicscalculationstosavethevaluesofthevelocitycomponentsoneachatomtoaseparatecyclefile.Thesefilesarewrittenwhenevertheatomiccoordinatesnapshotsarewrittenduringthedynamicsrun.Eachvelocityfilenamecontainsasasuffixthecyclenumberfollowedbytheletterv.


SLOPEMAX[real]Thiskeywordanditsmodifyingvaluesetthemaximumallowedsizeoftheratiobetween the current and initial projected gradients during the line search phase of conjugategradient or truncatedNewton optimizations. If this ratio exceedsSLOPEMAX, then the initial stepsizeisreducedbyafactorof10.Thedefaultvalueisusuallysetto10000.0whennotspecifiedviatheSLOPEMAXkeyword. SMOOTHING [DEM/GDA/TOPHAT/STOPHAT] This keyword activates the potential energysmoothingmethods. Several variations areavailable depending on the value of themodifier used:DEM= Diffusion Equation Method with a standard Gaussian kernel; GDA= Gaussian DensityAnnealingasproposedbytheStraubgroup;TOPHAT=alocalDEM-likemethodusingafiniterange``tophat''kernel;STOPHAT=shiftedtophatsmoothing. SOLVATE [ASP/SASA/ONION/STILL/HCT/ACE/GBSA] Use of this keyword during energycalculationswithanyofthestandardforcefieldsturnsonacontinuumsolvationfreeenergyterm.Severalalgorithmsareavailablebasedonthemodifierused:ASP=Eisenberg-McLachlanASPmethodusing theWesson-Eisenberg vacuum-to-water parameters; SASA= theOoi-Scheraga SASAmethod;ONION= the original 1990 Still ``Onion-shell'' GB/SA method; STILL= the 1997 analytical GB/SAmethodfromStill'sgroup;HCT=thepairwisedescreeningmethodofHawkins,CramerandTruhlar;ACE= the Analytical Continuum Electrostatics solvation method from the Karplus group; GBSA=equivalenttotheSTILLmodifier.Atpresent,GB/SA-stylemethodsareonlyvalidforforcefieldsthatusesimplepartialchargeelectrostatics. SOLVATETERM[NONE/ONLY]Thiskeywordcontrolsuseofthemacroscopicsolvationpotentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONE option turns off use of this potential energy term. The ONLY option turns off all potentialenergytermsexceptforthisone. SPACEGROUP[name]Thiskeywordselectsthespacegrouptobeusedinmanipulationofcrystalunitcellsandasymmetricunits.Thenameoptionmustbechosenfromoneofthefollowingcurrentlyimplementedspacegroups:P1,P1(-),P21,Cc,P21/a,P21/n,P21/c,C2/c,P212121,Pna21,Pn21a,Cmc21,Pccn,Pbcn,Pbca,P41,I41/a,P4(-)21c,P4(-)m2,R3c,P6(3)/mcm,Fm3(-)m,Im3(-)m. SPHERE[4reals,or1integer&1real]ThiskeywordprovidesanalternativetotheACTIVEandINACTIVEkeywords for specificationof subsetsofactiveatoms. If four realnumbermodifiersareprovided,thefirstthreearetakenasX-,Y-andZ-coordinatesandthefourthistheradiusofaspherecenteredatthesecoordinates.Inthiscase,allatomswithinthesphereatthestartofthecalculationareactivethroughoutthecalculation,whileallotheratomsareinactive.Similarlyifoneintegerandrealnumberaregiven,an``active''spherewithradiussetbytherealiscenteredonthesystematomwithatomnumbergivenbytheintegermodifier.MultipleSPHEREkeywordlinescanbepresentinasinglekeyfile,andthelistofactiveatomsspecifiedbythespheresiscumulative. STEEPEST-DESCENTThiskeywordforcestheL-BFGSoptimizationroutineusedbytheMINIMIZEprogramandotherprogramstoperformsteepestdescentminimization.Thisoptioncanbeusefulinconjunctionwithsmallstepsizesforfollowingminimumenergypaths,butisgenerallyinferiortotheL-BFGSdefaultformostoptimizationpurposes. STEPMAX[real]ThiskeywordanditsmodifyingvaluesetthemaximumsizeofanindividualstepduringthelinesearchphaseofconjugategradientortruncatedNewtonoptimizations.Thestepsizeiscomputedasthenormofthevectorofchangesinparametersbeingoptimized.Thedefaultvaluedepends on the particular TINKERprogram, but is usually in the range from1.0 to 5.0whennotspecifiedviatheSTEPMAXkeyword.


STEPMIN[real]ThiskeywordanditsmodifyingvaluesettheminimumsizeofanindividualstepduringthelinesearchphaseofconjugategradientortruncatedNewtonoptimizations.Thestepsizeiscomputedasthenormofthevectorofchangesinparametersbeingoptimized.Thedefaultvalueisusuallysettoabout10-16whennotspecifiedviatheSTEPMINkeyword. STRBND[1integer&3reals] Thiskeywordprovidesthevaluesforasinglestretch-bendcrosstermpotentialparameter.Theintegermodifiergivestheatomclassnumberforthecentralatomofthe bond angle involved in stretch-bend interactions. The real number modifiers give the forceconstant values to be usedwhen the central atomof the angle is attached to 0, 1 or 2 additionalhydrogenatoms,respectively.Thedefaultunitsforthestretch-bendforceconstantarekcal/mole/≈-degree,butthiscanbecontrolledviatheSTRBNDUNITkeyword. STRBNDTERM[NONE/ONLY] Thiskeywordcontrolsuseof thebondstretching-anglebendingcrosstermpotentialenergy.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. STRBNDUNIT[real] Sets thescalefactorneeded toconvert theenergyvaluecomputedby thebondstretching-anglebendingcrosstermpotentialintounitsofkcal/mole.Thecorrectvalueisforcefield dependentand typically provided in the header of themaster force field parameter file. Thedefaultvalueof1.0isused,iftheSTRBNDUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. STRTORS [2 integers&1 real] This keywordprovides the values for a single stretch-torsioncrosstermpotentialparameter.Thetwointegermodifiersgivetheatomclassnumbersfortheatomsinvolvedinthecentralbondofthetorsionalanglestobeparameterized.Therealmodifiergivesthevalueofthestretch-torsionforceconstantforalltorsionalangleswiththedefinedcentralbondatomclasses. The default units for the stretch-torsion force constant can be controlled via theSTRTORUNITkeyword. STRTORTERM[NONE/ONLY] Thiskeywordcontrolsuseofthebondstretching-torsionalanglecrosstermpotentialenergy.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. STRTORUNIT[real] Sets thescale factorneeded toconvert theenergyvaluecomputedby thebond stretching-torsional angle cross term potential into units of kcal/mole. The correct value isforcefielddependentandtypicallyprovidedintheheaderofthemasterforcefieldparameterfile.Thedefaultvalueof1.0isused,iftheSTRTORUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. TAPER[real] Thiskeywordallowsmodificationofthecutoffwindowsfornonbondedpotentialenergy interactions.Thenonbonded termsaresmoothly reduced fromtheir standardvalueat thebeginningofthecutoffwindowtozeroatthefarendofthewindow.Thefarendofthewindowisspecified via the CUTOFF keyword or its potential function specific variants. The modifier valuesuppliedwiththeTAPERkeywordsetsthebeginningofthecutoffwindow.Themodifiercanbegiveneither as an absolute distance value in Angstroms, or as a fraction between zero and one of theCUTOFFdistance.ThedefaultvalueintheabsenceoftheTAPERkeywordrangesfrom0.65to0.9oftheCUTOFFdistancedependingonthetypeofpotentialfunction.Thewindowsareimplementedviapolynomial-basedswitchingfunctions,insomecasescombinedwithenergyshifting.


TAU-PRESSURE[real]SetsthecouplingtimeinpicosecondsfortheGroningen-stylepressurebathcouplingusedtocontrolthesystempressureduringmoleculardynamicscalculations.Adefaultvalueof2.0isusedforTAU-PRESSUREintheabsenceofthekeyword. TAU-TEMPERATURE [real] Sets the coupling time in picoseconds for the Groningen-styletemperature bath coupling used to control the system temperature during molecular dynamicscalculations.Adefaultvalueof0.1isusedforTAU-TEMPERATUREintheabsenceofthekeyword. THERMOSTAT[BERENDSEN/ANDERSEN] Thiskeywordselectsathermostatalgorithmforuseduringmoleculardynamics.Twomodifiersareavailable,aBerendsenbathcouplingmethod,andanAndersenstochasticcollisionmethod.ThedefaultintheabsenceoftheTHERMOSTATkeywordistousetheBERENDSENalgorithm. TORSION[4integers&upto6real/real/integertriples]Thiskeywordprovidesthevaluesforasingletorsionalangleparameter.Thefirstfourintegermodifiersgivetheatomclassnumbersforthe atoms involved in the torsional angle to be defined. Each of the remaining triples ofreal/real/integermodifiersgivetheamplitude,phaseoffsetindegreesandperiodicityofaparticulartorsional function term, respectively. Periodicities through 6-fold are allowed for torsionalparameters. TORSION4[4integers&upto6real/real/integertriples]Thiskeywordprovidesthevaluesfora single torsional angle parameter specific to atoms in 4-membered rings. The first four integermodifiersgive theatomclassnumbers for theatoms involved in the torsionalangle tobedefined.The remaining triples of real number and integer modifiers operate as described above for theTORSIONkeyword. TORSION5[4integers&upto6real/real/integertriples]Thiskeywordprovidesthevaluesfora single torsional angle parameter specific to atoms in 5-membered rings. The first four integermodifiersgive theatomclassnumbers for theatoms involved in the torsionalangle tobedefined.The remaining triples of real number and integer modifiers operate as described above for theTORSIONkeyword. TORSIONTERM[NONE/ONLY]Thiskeywordcontrolsuseofthetorsionalanglepotentialenergyterm. In theabsenceofamodifyingoption, thiskeyword turnsonuseof thepotential.TheNONEoption turns off use of this potential energy term. TheONLYoption turns off all potential energytermsexceptforthisone. TORSIONUNIT[real] Setsthescalefactorneededtoconverttheenergyvaluecomputedbythetorsional angle potential into units of kcal/mole. The correct value is force field dependent andtypicallyprovidedintheheaderofthemasterforcefieldparameterfile.Thedefaultvalueof1.0isused,iftheTORSIONUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. TORTOR[7 integers, thenmultiple linesof2 integersand1real] Thiskeyword isused toprovide the values for a single torsion-torsionparameter. The first five integermodifiers give theatomclassnumbersfortheatomsinvolvedinthetwoadjacenttorsionalanglestobedefined.Thelast two integermodifiers contain the number of data grid points that lie along each axis of thetorsion-torsionmap.Forexample,thisvaluewillbe13fora30degreetorsionalanglespacing, i.e.,360/30=12,but13valuesarerequiredsincedatavaluesfor-180and+180degreesmustbothbesupplied.Thesubsequentlinescontainthetorsion-torsionmapdataastheintegervaluesindegreesofeachtorsionalangleandthetargetenergyvalueinkcal/mole.


TORTORTERM[NONE/ONLY]Thiskeywordcontrolsuseofthetorsion-torsionpotentialenergyterm. In theabsenceofamodifyingoption, thiskeyword turnsonuseof thepotential.TheNONEoption turns off use of this potential energy term. TheONLYoption turns off all potential energytermsexceptforthisone. TORTORUNIT[real] Setsthescalefactorneededtoconverttheenergyvaluecomputedbythetorsion-torsion potential into units of kcal/mole. The correct value is force field dependent andtypicallyprovidedintheheaderofthemasterforcefieldparameterfile.Thedefaultvalueof1.0isused,iftheTORTORUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. TRIAL-DISTANCE[CLASSIC/RANDOM/TRICOR/HAVELinteger/PAIRWISEinteger]Setsthe method for selection of a trial distance matrix during distance geometry computations. Thekeywordtakesamodifierthatselectsthemethodtobeused.TheHAVELandPAIRWISEmodifiersalsorequireanadditionalintegervaluethatspecifiesthenumberofatomsusedinmetrizationandthepercentageofmetrization,respectively.ThedefaultintheabsenceofthiskeywordistousethePAIRWISE method with 100 percent metrization. Further information on the variousmethods isgivenwiththedescriptionoftheTINKERdistancegeometryprogram. TRIAL-DISTRIBUTION[real]SetstheinitialvalueforthemeanoftheGaussiandistributionusedto select trial distances between the lower and upper bounds during distance geometrycomputations. The value given must be between 0 and 1 which represent the lower and upperboundsrespectively.Thiskeyword is rarelyneededsinceTINKERwillusuallybeable tochooseareasonablevaluebydefault. TRUNCATECausesalldistance-basednonbondenergycutoffstobesharplytruncatedtoanenergyofzeroatdistancesgreaterthanthevaluesetbythecutoffkeyword(s)withoutuseofanyshifting,switchingorsmoothingschemes.Atalldistanceswithinthecutoffsphere,thefullinteractionenergyiscomputed. UREY-CUBIC [real] Sets thevalueof thecubic term in theTaylorseriesexpansion formof theUrey-Bradley potential energy. The real number modifier gives the value of the coefficient as amultipleofthequadraticcoefficient.ThedefaultvalueintheabsenceoftheUREY-CUBICkeywordiszero;i.e.,thecubicUrey-Bradleytermisomitted. UREY-QUARTIC[real]SetsthevalueofthequartictermintheTaylorseriesexpansionformoftheUrey-Bradley potential energy. The real number modifier gives the value of the coefficient as amultipleofthequadraticcoefficient.ThedefaultvalueintheabsenceoftheUREY-QUARTICkeywordiszero;i.e.,thequarticUrey-Bradleytermisomitted. UREYBRAD[3integers&2reals] ThiskeywordprovidesthevaluesforasingleUrey-Bradleycross term potential parameter. The integermodifiers give the atom class numbers for the threekindsofatomsinvolvedintheangleforwhichaUrey-Bradleytermistobedefined.Therealnumbermodifiersgivetheforceconstantvalueforthetermandthetargetvalueforthe1-3distancein≈.Thedefaultunitsfortheforceconstantarekcal/mole/≈2,butthiscanbecontrolledviatheUREYUNITkeyword. UREYTERM[NONE/ONLY]ThiskeywordcontrolsuseoftheUrey-Bradleypotentialenergyterm.Intheabsenceofamodifyingoption,thiskeywordturnsonuseofthepotential.TheNONEoptionturns off use of this potential energy term. The ONLYoption turns off all potential energy termsexceptforthisone.


UREYUNIT[real]SetsthescalefactorneededtoconverttheenergyvaluecomputedbytheUrey-Bradley potential into units of kcal/mole. The correct value is force field dependent and typicallyprovidedintheheaderofthemasterforcefieldparameterfile.Thedefaultvalueof1.0isused,iftheUREYUNITkeywordisnotgivenintheforcefieldparameterfileorthekeyfile. VDW[1integer&3reals] ThiskeywordprovidesvaluesforasinglevanderWaalsparameter.Theintegermodifier, ifpositive,gives theatomclassnumberforwhichvdwparametersare tobedefined.Notethatvdwparametersaregivenforatomclasses,notatomtypes.Thethreerealnumbermodifiersgivethevaluesoftheatomsizein≈,homoatomicwelldepthinkcal/mole,andanoptionalreductionfactorforunivalentatoms. VDW-12-SCALE[real] ThiskeywordprovidesamultiplicativescalefactorthatisappliedtovanderWaalspotential interactionsbetween1-2connectedatoms, i.e.,atomsthataredirectlybonded.Thedefaultvalueof0.0isused,iftheVDW-12-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. VDW-13-SCALE[real] ThiskeywordprovidesamultiplicativescalefactorthatisappliedtovanderWaalspotentialinteractionsbetween1-3connectedatoms,i.e.,atomsseparatedbytwocovalentbonds. The default value of 0.0 is used, if the VDW-13-SCALE keyword is not given in either theparameterfileorthekeyfile. VDW-14-SCALE[real] Thiskeywordprovidesamultiplicativescalefactorthatisappliedtovander Waals potential interactions between 1-4 connected atoms, i.e., atoms separated by threecovalentbonds.Thedefaultvalueof1.0isused,iftheVDW-14-SCALEkeywordisnotgivenineithertheparameterfileorthekeyfile. VDW-15-SCALE[real] ThiskeywordprovidesamultiplicativescalefactorthatisappliedtovanderWaalspotentialinteractionsbetween1-5connectedatoms,i.e.,atomsseparatedbyfourcovalentbonds. The default value of 1.0 is used, if the VDW-15-SCALE keyword is not given in either theparameterfileorthekeyfile. VDW-CUTOFF [real] Sets the cutoff distance value in Angstroms for van derWaals potentialenergyinteractions.TheenergyforanypairofvanderWaalssitesbeyondthecutoffdistancewillbesettozero.Otherkeywordscanbeusedtoselectasmoothingschemenearthecutoffdistance.Thedefault cutoff distance in the absence of the VDW-CUTOFF keyword is infinite for nonperiodicsystemsand9.0forperiodicsystems. VDW-TAPER[real] Thiskeywordallowsmodificationof thecutoffwindows forvanderWaalspotentialenergyinteractions.ItissimilarinformandactiontotheTAPERkeyword,exceptthatitsvalueappliesonlytothevdwpotential.ThedefaultvalueintheabsenceoftheVDW-TAPERkeywordistobeginthecutoffwindowat0.9ofthevdwcutoffdistance. VDW14[1integer&2reals]ThiskeywordprovidesvaluesforasinglevanderWaalsparameterforusein1-4nonbondedinteractions.Theintegermodifier,ifpositive,givestheatomclassnumberforwhichvdwparametersaretobedefined.Notethatvdwparametersaregivenforatomclasses,not atom types. The two real number modifiers give the values of the atom size in ≈ and thehomoatomic well depth in kcal/mole. Reduction factors, if used, are carried over from the VDWkeywordforthesameatomclass. VDWPR[2integers&2reals] Thiskeywordprovidesthevaluesforthevdwparametersforasinglespecialheteroatomicpairofatoms.Theintegermodifiersgivethepairofatomclassnumbers


forwhichspecialvdwparametersaretobedefined.Thetworealnumbermodifiersgivethevaluesoftheminimumenergycontactdistancein≈andthewelldepthattheminimumdistanceinkcal/mole. VDWTERM[NONE/ONLY]ThiskeywordcontrolsuseofthevanderWaalsrepulsion-dispersionpotential energy term. In the absence of a modifying option, this keyword turns on use of thepotential.TheNONEoptionturnsoffuseofthispotentialenergyterm.TheONLYoptionturnsoffallpotentialenergytermsexceptforthisone. VDWTYPE [LENNARD-JONES / BUCKINGHAM / BUFFERED-14-7 /MM3-HBOND / GAUSSIAN]Sets the functional form for the vanderWaals potential energy term. The textmodifier gives thename of the functional form to be used. TheGAUSSIANmodifier value implements a two or fourGaussian fit to thecorrespondingLennard-Jones function forusewithpotentialenergysmoothingschemes.ThedefaultintheabsenceoftheVDWTYPEkeywordistousethestandardtwoparameterLennard-Jonesfunction. VERBOSE Turnsonprintingof secondaryand informationaloutputduringavarietyofTINKERcomputations;asubsetofthemoreextensiveoutputprovidedbytheDEBUGkeyword. WALL [real] Sets the radius of a spherical boundary used to maintain droplet boundaryconditions.Therealmodifierspecifiesthedesiredapproximateradiusofthedroplet.Inpractice,anartificialvanderWaalswall isconstructedatafixedbufferdistanceof2.5≈outside thespecifiedradius. The effect is that atomswhich attempt tomove outside the regiondefinedby the dropletradiuswillbeforcedtowardthecenter. WRITEOUT[integer] Ageneralparameter for iterativeproceduressuchasminimizations thatsets the number of iterations between writes of intermediate results (such as the currentcoordinates)todiskfile(s).Thedefaultvalueintheabsenceofthekeywordis1,i.e.,theintermediateresultsarewritten to fileonevery iteration.Whethersuccessiveintermediate resultsaresaved tonew files or replace previouslywritten intermediate results is controlled by theOVERWRITE andSAVE-CYCLEkeywords.


8. ForceFieldParameterSets TheTINKERpackageisdistributedwithseveralforcefieldparametersets,implementingaselectionofwidelyusedliteratureforcefieldsaswellastheTINKERforcefieldcurrentlyunderconstructioninthe Ponder lab.We try to exactly reproduce the intent of the original authors of our distributed,third-partyforcefields.Inallcasestheparametersetshavebeenvalidatedagainstliteraturereports,resultsprovidedbytheoriginaldevelopers,orcalculationsmadewiththeauthenticprograms.Withthe fewexceptionsnotedbelow,TINKERcalculationscanbe treatedasauthentic results fromthegenuineforcefields.Abriefdescriptionofeachparameterset,includingsomestillinpreparationandnotdistributedwith thecurrentversion, isprovidedbelowwith lead literature references for theforcefield: AMOEBA.PRM Parameters for the AMOEBA polarizable atomic multipole force field. As of the current TINKERrelease,wehavecompletedparametrizationforanumberof ionsandsmallorganicmolecules.Forfurther information, or if you are interested in developing or testing parameters for other smallmolecules,pleasecontactthePonderlab. P. Ren and J. W. Ponder, A Consistent Treatment of Inter- and Intramolecular Polarization inMolecularMechanicsCalculations,J.Comput.Chem.,23,1497-1506(2002) P. Ren and J. W. Ponder, Polarizable Atomic Multipole Water Model for Molecular MechanicsSimulation,J.Phys.Chem.B,107,5933-5947(2003) P.Ren and J.W. Ponder, Ion SolvationThermodynamics fromSimulationwitha PolarizableForceField,A.Grossfield,J.Am.Chem.Soc.,125,15671-15682(2003) AMOEBAPRO.PRM PreliminaryproteinparametersfortheAMOEBApolarizableatomicmultipoleforcefield.Whilethedistributedparametersarestillsubjecttominoralterationaswecontinuevalidation,theyarenowstableenoughforothergroupstobeginusingthem.Forfurtherinformation,orifyouareinterestedintestingtheproteinparameterset,pleasecontactthePonderlab. J.W.PonderandD.A.Case,ForceFieldsforProteinSimulation,Adv.Prot.Chem.,66,27-85(2003) P.RenandJ.W.Ponder,PolarizableAtomicMultipole-basedPotentialforProteins:ModelandParameterization,inpreparation AMBER94.PRM AMBERff94parametersforproteinsandnucleicacids.Notethatwiththeir``Cornell''forcefield,theKollmangrouphasdevisedseparate,fullyindependentpartialchargevaluesforeachoftheN-andC-terminalaminoacidresidues.Atpresent,theterminalresiduechargesforTINKER'sversionmaintainthecorrectformalcharge,butredistributedsomewhatatthealphacarbonatomsfromtheoriginalKollmangroupvalues.Thetotalmagnitudeoftheredistributionis lessthan0.01electronsinmostcases. W.D.Cornell,P.Cieplak,C.I.Bayly,I.R.Gould,K.M.Merz,Jr.,D.M.Ferguson,D.C.Spellmeyer,T.Fox,J.W. Caldwell andP. A. Kollman,A SecondGeneration Force Field for the Simulation of Proteins,NucleicAcids,andOrganicMolecules,J.Am.Chem.Soc.,117,5179-5197(1995)[ff94]


G.Moyna,H. J.Williams,R. J.NachmanandA.I.Scott,ConformationinSolutionandDynamicsofaStructurally Constrained Linear Insect Kinin Pentapeptide Analogue, Biopolymers, 49, 403-413(1999)[AIBcharges] W. S. Ross and C. C. Hardin, Ion-Induced Stabilization of the G-DNA Quadruplex: Free EnergyPerturbationStudies,J.Am.Chem.Soc.,116,4363-4366(1994)[alkalimetalions] J. Aqvist, Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations, J.Phys.Chem.,94,8021-8024,1990[alkalineearthIons,radiiadaptedforAmbercombiningrule] Current forcefieldparametervaluesandsuggestedprocedures fordevelopmentofparametersforadditional molecules are available from the Amber web site in the Case lab at Scripps,http://amber.scripps.edu/ AMBER96.PRM AMBERff96parametersforproteinsandnucleicacids.Theonlychangefromtheff94parametersetisinthetorsionalparametersfortheproteinphi/psiangles.Thesevalueswerealteredtogivebetteragreementwith changesof ff96withLMP2QMresultsfromtheFriesner labonalaninedipeptideandtetrapeptide. P.Kollman,R.Dixon,W.Cornell,T.Fox,C.ChipotandA.Pohorille,TheDevelopment/Applicationofa'Minimalist'Organic/BiochemicalMolecularMechanicForceFieldusingaCombinationofab InitioCalculationsandExperimentalData,inComputerSimulationofBiomolecularSystems,W.F.vanGunsteren,P.K.Weiner,A.J.Wilkinson,eds.,Volume3,83-96(1997)[ff96] Current forcefieldparametervaluesandsuggestedprocedures fordevelopmentofparametersforadditional molecules are available from the Amber web site in the Case lab at Scripps,http://amber.scripps.edu/ AMBER98.PRM AMBERff98parametersforproteinsandnucleicacids.Theonlychangefromtheff94parametersetisintheglycosidictorsionalparametersthatcontrolsugarpucker. T.E.CheathamIII,P.CieplakandP.A.Kollman,AModifiedVersionoftheCornelletal.ForceFieldwithImprovedSugarPuckerPhasesandHelicalRepeat,J.Biomol.Struct.Dyn.,16,845-862(1999) Current forcefieldparametervaluesandsuggestedprocedures fordevelopmentofparametersforadditional molecules are available from the Amber web site in the Case lab at Scripps,http://amber.scripps.edu/ AMBER99.PRM AMBER ff99 parameters for proteins and nucleic acids. The original partial charges from the ff94parametersetareretained,butmanyofthebond,angleandtorsionalparametershavebeenrevisedtoprovidebettergeneralagreementwithexperiment. J.Wang, P. Cieplak andP. A. Kollman,HowWellDoes aRestrainedElectrostatic Potential (RESP)Model Perform in Calcluating Conformational Energies of Organic and Biological Molecules?, J.Comput.Chem.,21,1049-1074(2000)


Current forcefieldparametervaluesandsuggestedprocedures fordevelopmentofparametersforadditional molecules are available from the Amber web site in the Case lab at Scripps,http://amber.scripps.edu/ CHARMM19.PRM CHARMM19 united-atom parameters for proteins. The nucleic acid parameter are not yetimplemented.TherearesomedifferencesbetweenauthenticCHARMM19and theTINKERversionduetoreplacementofCHARMMimpropersbytorsionsforcasesthat involveatomsnotbondedtothetrigonalatomandTINKER'suseofallpossibletorsionsacrossabondinsteadofasingletorsionperbond. E.Neria,S.FischerandM.Karplus,SimulationofActivationFreeEnergies inMolecularSystems, J.Chem.Phys.,105,1902-1921(1996) L.Nilsson andM.Karplus, Empirical Energy Functions for EnergyMinimizations andDynamics ofNucleicAcids,J.Comput.Chem.,7,591-616(1986) W.E. Reiher III, Theoretical Studies ofHydrogenBonding, Ph.D. Thesis,Department ofChemistry,HarvardUniversity,Cambridge,MA,1985 CHARMM22.PRM CHARMM27all-atomparameters forproteinsand lipids.Mostof thenucleicacidandsmallmodelcompoundparametersarenotyetimplemented.Weplantoprovidetheseadditionalparametersinduecourse. N.FoloppeandA.D.MacKerell, Jr.,All-AtomEmpiricalForceField forNucleicAcids:1)ParameterOptimizationBasedonSmallMoleculeandCondensedPhaseMacromolecularTargetData,J.Comput.Chem.,21,86-104(2000)[CHARMM27] N.BanavaliandA.D.MacKerell,Jr.,All-AtomEmpiricalForceFieldforNucleicAcids:2)Applicationto Molecular Dynamics Simulations of DNA and RNA in Solution, J. Comput. Chem., 21, 105-120(2000) A.D.MacKerrell,Jr.,etal.,All-AtomEmpiricalPotentialforMolecularModelingandDynamicsStudiesofProteins,J.Phys.Chem.B,102,3586-3616(1998)[CHARMM22] A.D.MacKerell, Jr., J.Wiorkeiwicz-KuczeraandM.Karplus,AnAll-AtomEmpiricalEnergyFunctionfortheSimulationofNucleicAcids,J.Am.Chem.Soc.,117,11946-11975(1995) S. E. Feller, D. Yin, R. W. Pastor and A. D. MacKerell, Jr., Molecular Dynamics Simulation ofUnsaturated Lipids at Low Hydration: Parametrization and Comparison with Diffraction Studies,BiophysicalJournal,73,2269-2279(1997)[alkenes] R.H.StoteandM.Karplus,ZincBindinginProteinsandSolution-ASimplebutAccurateNonbondedRepresentation,Proteins,23,12-31(1995)[zincion] Currentand legacyparametervaluesareavailable fromtheCHARMMforce fieldwebsiteonAlexMacKerell's Research Interests page at the University of Maryland School of Pharmacy,https://rxsecure.umaryland.edu/research/amackere/research.html/ DUDEK.PRM


Protein-onlyparametersfortheearly1990'sTINKERforcefieldwithmultipolevaluesofDudekandPonder. The current file contains only the multipole values from the 1995 paper by Dudek andPonder.This set isnowsuperceededby themorerecentTINKER force fielddevelopedbyPengyuRen(seeWATER.PRM,below). M. J. Dudek and J. W. Ponder, Accurate Electrostatic Modelling of the Intramolecular Energy ofProteins,J.Comput.Chem.,16,791-816(1995) ENCAD.PRM ENCADparametersforproteinsandnucleicacids.(inpreparation) M. Levitt, M. Hirshberg, R. Sharon and V. Daggett, Potential Energy Function and Parameters forSimulations of the Molecular Dynamics of Protein and Nucleic Acids in Solution, Comp. Phys.Commun.,91,215-231(1995) M. Levitt,M.Hirshberg, R. Sharon,K. E. Laidig andV.Daggett, Calibration andTesting of aWaterModel for Simulation of theMolecularDynamics of Protein andNucleicAcids in Solution, J. Phys.Chem.B,101,5051-5061(1997)[F3Cwater] HOCH.PRM SimpleNMR-NOEforcefieldofHochandStern. J. C. Hoch and A. S. Stern, A Method for Determining Overall Protein Fold from NMR DistanceRestraints,J.Biomol.NMR,2,535-543(1992) MM2.PRM Full MM2(1991) parameters including p-systems. The anomeric and electronegativity correctiontermsincludedinsomelaterversionsofMM2arenotimplemented. N.L.Allinger,ConformationalAnalysis.130.MM2.AHydrocarbonForceFieldUtilizingV1andV2TorsionalTerms,J.Am.Chem.Soc.,99,8127-8134(1977) J.T.Sprague,J.C.Tai,Y.YuhandN.L.Allinger,TheMMP2CalculationalMethod,J.Comput.Chem.,8,581-603(1987) J. C. Tai and N. L. Allinger, Molecular Mechanics Calculations on Conjugated Nitrogen-ContainingHeterocycles,J.Am.Chem.Soc.,110,2050-2055(1988) J.C.Tai, J.-H.Lii andN.L.Allinger,AMolecularMechanics (MM2)StudyofFuran,Thiophene,andRelatedCompounds,J.Comput.Chem.,10,635-647(1989) N.L.Allinger,R.A.KokandM.R.Imam,HydrogenBondinginMM2,J.Comput.Chem.,9,591-595(1988) L.Norskov-LauritsenandN.L.Allinger,AMolecularMechanicsTreatmentoftheAnomericEffect,J.Comput.Chem.,5,326-335(1984) AllparametersdistributedwithTINKERarefromthe``MM2(1991)ParameterSet'',asprovidedbyN.L.Allinger,UniversityofGeorgia


MM3.PRM Full MM3(2000) parameters including pi-systems. The directional hydrogen bonding term andelectronegativity bond length corrections are implemented, but the anomeric and Bohlmanncorrectiontermsarenotimplemented. N.L.Allinger,Y.H.YuhandJ.-H.Lii,MolecularMechanics.TheMM3ForceFieldforHydrocarbons.1,J.Am.Chem.Soc.,111,8551-8566(1989) J.-H. Lii and N. L. Allinger, Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 2.VibrationalFrequenciesandThermodynamics,J.Am.Chem.Soc.,111,8566-8575(1989) J.-H.LiiandN.L.Allinger,MolecularMechanics.TheMM3ForceFieldforHydrocarbons.3.ThevanderWaals'PotentialsandCrystalDataforAliphaticandAromaticHydrocarbons,J.Am.Chem.Soc.,111,8576-8582(1989) N.L.Allinger,H.J.Geise,W.Pyckhout,L.A.PaquetteandJ.C.Gallucci,StructuresofNorbornaneandDodecahedrane by Molecular Mechanics Calculations (MM3), X-ray Crystallography, and ElectronDiffraction,J.Am.Chem.Soc.,111,1106-1114(1989)[stretch-torsioncrossterm] N.L.Allinger,F.LiandL.Yan,MolecularMechanics.TheMM3ForceField forAlkenes, J.Comput.Chem.,11,848-867(1990) N. L. Allinger, F. Li, L. Yan and J. C. Tai, Molecular Mechanics (MM3) Calculations on ConjugatedHydrocarbons,J.Comput.Chem.,11,868-895(1990) J.-H. Lii and N. L. Allinger,Directional Hydrogen Bonding in theMM3Force Field. I, J. Phys. Org.Chem.,7,591-609(1994) J.-H.LiiandN.L.Allinger,DirectionalHydrogenBondingintheMM3ForceField.II,J.Comput.Chem.,19,1001-1016(1998) AllparametersdistributedwithTINKERarefromthe``MM3(2000)ParameterSet'',asprovidedbyN.L.Allinger,UniversityofGeorgia,August2000 MM3PRO.PRM Protein-onlyversionoftheMM3parameters. J.-H.Lii andN.L.Allinger,TheMM3ForceField forAmides,PolypeptidesandProteins, J.Comput.Chem.,12,186-199(1991) OPLSUA.PRM CompleteOPLS-UAwithunited-atomparametersforproteinsandmanyclassesoforganicmolecules.Explicithydrogensonpolaratomsandaromaticcarbons. W.L.JorgensenandJ.Tirado-Rives,TheOPLSPotentialFunctionsforProteins.EnergyMinimizationsforCrystalsofCyclicPeptidesandCrambin,J.Am.Chem.Soc.,110,1657-1666(1988)[peptideandproteins]


W.L. Jorgensen andD. L. Severance, Aromatic-Aromatic Interactions: FreeEnergyProfiles for theBenzeneDimerinWater,Chloroform,andLiquidBenzene,J.Am.Chem.Soc.,112,4768-4774(1990)[aromatichydrogens] S.J.Weiner,P.A.Kollman,D.A.Case,U.C.Singh,C.Ghio,G.Alagona,S.Profeta,Jr.andP.Weiner,ANewForce Field forMolecularMechanical Simulation ofNucleicAcidsandProteins, J. Am. Chem.Soc.,106,765-784(1984)[united-atom``AMBER/OPLS''localgeometry] S. J.Weiner,P.A.Kollman,D.T.NguyenandD.A.Case,AnAllAtomForceFieldforSimulationsofProteins and Nucleic Acids, J. Comput. Chem., 7, 230-252 (1986) [all-atom "AMBER/OPLS" localgeometry] L.X.Dang andB.M. Pettitt, Simple IntramolecularModel Potentials forWater, J. Phys. Chem.,91,3349-3354(1987)[flexibleTIP3PandSPCwater] W.L. Jorgensen, J.D.Madura andC. J. Swenson,Optimized Intermolecular Potential Functions forLiquidHydrocarbons,J.Am.Chem.Soc.,106,6638-6646(1984)[hydrocarbons] W.L.Jorgensen,E.R.Laird,T.B.NguyenandJ.Tirado-Rives,MonteCarloSimulationsofPureLiquidSubstituted Benzenes with OPLS Potential Functions, J. Comput. Chem., 14, 206-215 (1993)[substitutedbenzenes] E. M. Duffy, P. J. Kowalczyk and W. L. Jorgensen, Do Denaturants Interact with AromaticHydrocarbons inWater?, J. Am. Chem. Soc.,115, 9271-9275 (1993) [benzene, naphthalene, urea,guanidinium,tetramethylammonium] W. L. Jorgensen and C. J. Swenson, Optimized Intermolecular Potential Functions for Amides andPeptides. Structure and Properties of Liquid Amides, J. Am. Chem. Soc., 106, 765-784 (1984)[amides] W.L. Jorgensen,J.M.BriggsandM.L.Contreras,RelativePartitionCoefficientsforOrganicSolutesform Fluid Simulations, J. Phys. Chem., 94, 1683-1686 (1990) [chloroform, pyridine, pyrazine,pyrimidine] J.M. Briggs, T. B.Nguyen andW. L. Jorgensen,MonteCarlo Simulations ofLiquidAceticAcid andMethylAcetatewiththeOPLSPotentialFunctions,J.Phys.Chem.,95,3315-3322(1991)[aceticacid,methylacetate] H. Liu,F.Muller-PlatheandW. F. vanGunsteren, A ForceField for LiquidDimethyl Sulfoxide andPhysicalPropertiesofLiquidDimethylSulfoxideCalculatedUsingMolecularDynamicsSimulation,J.Am.Chem.Soc.,117,4363-4366(1995)[dimethylsulfoxide] J. Gao, X. Xia and T. F. George, Importance of Bimolecular Interactions in Developing EmpiricalPotentialFunctionsforLiquidAmmonia,J.Phys.Chem.,97,9241-9246(1993)[ammonia] J. Aqvist, Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations, J.Phys.Chem.,94,8021-8024(1990)[metalions] W. S. Ross and C. C. Hardin, Ion-Induced Stabilization of the G-DNA Quadruplex: Free EnergyPerturbationStudies,J.Am.Chem.Soc.,116,4363-4366(1994)[alkalimetalions] J. Chandrasekhar, D. C. Spellmeyer and W. L. Jorgensen, Energy Component Analysis for DiluteAqueousSolutionsofLi+,Na+,F-,andCl-Ions,J.Am.Chem.Soc.,106,903-910(1984)[halideions]


Most parameters distributedwith TINKER are from ``OPLS and OPLS-AA Parameters for OrganicMolecules,Ions,andNucleicAcids''asprovidedbyW.L.Jorgensen,YaleUniversity,October1997 OPLSAA.PRM OPLS-AA force field with all-atom parameters for proteins and many general classes of organicmolecules. W.L. Jorgensen,D.S.Maxwelland J.Tirado-Rives,DevelopmentandTestingof theOPLSAll-AtomForceFieldonConformationalEnergeticsandPropertiesofOrganicLiquids,J.Am.Chem.Soc.,117,11225-11236(1996) D.S.Maxwell,J.Tirado-RivesandW.L.Jorgensen,AComprehensiveStudyoftheRotationalEnergyProfiles of Organic Systems by Ab Initio MO Theory, Forming a Basis for Peptide TorsionalParameters,J.Comput.Chem.,16,984-1010(1995) W. L. Jorgensen and N. A. McDonald, Development of an All-Atom Force Field for Heterocycles.PropertiesofLiquidPyridineandDiazenes,THEOCHEM-J.Mol.Struct.,424,145-155(1998) N. A. McDonald and W. L. Jorgensen, Development of an All-Atom Force Field for Heterocycles.PropertiesofLiquidPyrrole,Furan,Diazoles,andOxazoles,J.Phys.Chem.B,102,8049-8059(1998) R.C.RizzoandW.L.Jorgensen,OPLSAll-AtomModelforAmines:ResolutionoftheAmineHydrationProblem,J.Am.Chem.Soc.,121,4827-4836(1999) M.L.P.Price,D.OstrovskyandW.L.Jorgensen,Gas-PhaseandLiquid-StatePropertiesofEsters,Nitriles,andNitroCompoundswiththeOPLS-AAForceField,J.Comput.Chem.,22,1340-1352(2001) All parameters distributed with TINKER are from ``OPLS and OPLS-AA Parameters for OrganicMolecules,Ions,andNucleicAcids''asprovidedbyW.L.Jorgensen,YaleUniversity,October1997 OPLSAAL.PRM AnimprovedOPLS-AAparametersetforproteinsinwhichtheonlychangeisareworkingofmanyofthe backbone and sidechain torsional parameters to give better agreement with LMP2 QMcalculations.ThisparametersetisalsoknownasOPLS(2000). G.A.Kaminsky,R.A.Friesner,J.Tirado-RivesandW.L.Jorgensen,EvaluationandReparametrizationof the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum ChemicalCalculationsonPeptides,J.Phys.Chem.B,105,6474-6487(2001) SMOOTH.PRM VersionofOPLS-UAforusewithpotentialsmoothing.LargelyadaptedlargelyfromstandardOPLS-UAparameterswithmodificationstothevdwandimpropertorsionterms. R.V.Pappu,R.K.HartandJ.W.Ponder,AnalysisandApplicationofPotentialEnergySmoothingandSearch Methods for Global Optimization, J. Phys, Chem. B, 102, 9725-9742 (1998) [smoothingmodifications] SMOOTHAA.PRM


VersionofOPLS-AAforusewithpotentialsmoothing.LargelyadaptedlargelyfromstandardOPLS-AAparameterswithmodificationstothevdwandimpropertorsionterms. R.V.Pappu,R.K.HartandJ.W.Ponder,AnalysisandApplicationofPotentialEnergySmoothingandSearch Methods for Global Optimization, J. Phys, Chem. B, 102, 9725-9742 (1998) [smoothingmodifications] WATER.PRM TheAMOEBAwaterparametersforapolarizableatomicmultipoleelectrostaticsmodel.Thismodelisequalorbettertothebestavailablewatermodelsformanybulkandclusterproperties. P. Ren and J. W. Ponder, A Polarizable Atomic Multipole Water Model for Molecular MechanicsSimulation,J.Phys.Chem.B,107,5933-5947(2003) P.Ren and J.W. Ponder, Ion SolvationThermodynamics fromSimulationwitha PolarizableForceField,A.Grossfield,J.Am.Chem.Soc.,125,15671-15682(2003) P. Ren and J.W. Ponder, Temperature and Pressure Dependence of the AMOEBAWaterModel, J.Phys.Chem.B,108,xxxx-xxxx(2004) An earlier version the AMOEBA water model is described in: Yong Kong, Multipole ElectrostaticMethodsforProteinModelingwithReactionFieldTreatment,Biochemistry&MolecularBiophysics,WashingtonUniversity,St.Louis,August,1997[availablefromhttp://dasher.wustl.edu/ponder/]


9. DescriptionsofTINKERRoutines ThedistributionversionoftheTINKERpackagecontainsover700separateprograms,subroutinesand functions.This sectioncontainsabriefdescriptionof thepurposeofmostof thesecodeunits.Furtherinformationcanbefoundinthecommentslocatedatthetopofeachsourcecodefile. ACTIVESubroutine "active"setsthelistofatomsthatareusedduringeachpotentialenergyfunctioncalculation ADDBASESubroutine "addbase"buildstheCartesiancoordinatesforasinglenucleicacidbase;coordinatesarereadfromthe Protein Data Bank file or found from internal coordinates, then atom types are assigned andconnectivitydatagenerated ADDBONDSubroutine "addbond"addsentriestotheattachedatomslistinordertogenerateadirectconnectionbetweentwoatoms ADDSIDESubroutine "addside"buildstheCartesiancoordinatesforasingleaminoacidsidechain;coordinatesarereadfromtheProteinDataBankfileorfoundfrominternalcoordinates,thenatomtypesareassignedandconnectivitydatagenerated ADJACENTFunction "adjacent"findsanatomconnectedtoatom"i1"otherthanatom"i2";ifnosuchatomexists,thentheclosestatominspaceisreturned ALCHEMYProgram "alchemy"computesthefreeenergydifferencecorrespondingtoasmallperturbationbyBoltzmannweighting the potential energy difference over a number of sample states; current version(incorrectly)considersthechargeenergytobeintermolecularinfindingtheperturbationenergies ANALYSISSubroutine "analysis" calls theseriesof routinesneeded tocalculate thepotentialenergyandperformenergypartitioninganalysisintermsoftypeofinteractionoratomnumber ANALYZ4Subroutine "analyz4"printstheenergyto4decimalplacesandnumberof interactionsforeachcomponentofthepotentialenergy ANALYZ6Subroutine


"analyz6"printstheenergyto6decimalplacesandnumberof interactionsforeachcomponentofthepotentialenergy ANALYZ8Subroutine "analyz8"printstheenergyto8decimalplacesandnumberof interactionsforeachcomponentofthepotentialenergy ANALYZEProgram "analyze"computesanddisplaysthetotalpotential;optionsareprovidedtopartitiontheenergybyatomorbypotentialfunctiontype;parametersusedincomputinginteractionscanalsobedisplayedbyatom;outputoflargeenergyinteractionsandofelectrostaticandinertialpropertiesisavailable ANGLESSubroutine "angles"findsthetotalnumberofbondanglesandstorestheatomnumbersoftheatomsdefiningeachangle;foreachangletoatrivalentcentralatom,thethirdbondedatomisstoredforuseinout-of-planebending ANNEALProgram "anneal" performs a simulated annealing protocol by means of variable temperature moleculardynamicsusingeitherlinear,exponentialorsigmoidalcoolingschedules ANORMFunction "anorm"findsthenorm(length)ofavector;usedasaserviceroutinebytheConnollysurfaceareaandvolumecomputation ARCHIVEProgram "archive"isautilityprogramforcoordinatefileswhichconcatenatesmultiplecoordinatesetsintoasinglearchivefile,orextractsindividualcoordinatesetsfromanarchive ASETSubroutine "aset" computes by recursion the A functions used in the evaluation of Slater-type (STO) overlapintegrals ATOMYZESubroutine "atomyze"printsthepotentialenergycomponentsbrokendownbyatomandtoachoiceofprecision ATTACHSubroutine "attach"generateslistsof1-3,1-4and1-5connectivitiesstartingfromthepreviouslydeterminedlistofattachedatoms(ie,1-2connectivity)


BASEFILESubroutine "basefile"extractsfromaninputfilenametheportionconsistingofanydirectorynameandthebasefilename BCUCOFSubroutine "bcucof"determinesthecoefficientmatrixneededforbicubic interpolationofafunction,gradientsandcrossderivatives BCUINTSubroutine "bcuint"performsabicubicinterpolationofthefunctionvalueona2Dsplinegrid BCUINT1Subroutine "bcuint1"performsabicubicinterpolationofthefunctionvalueandgradientalongthedirectionsofa2Dsplinegrid BCUINT2Subroutine "bcuint2" performs a bicubic interpolation of the function value, gradient and Hessain along thedirectionsofa2Dsplinegrid BEEMANSubroutine "beeman"performsasinglemoleculardynamicstimestepbymeansofaBeemanmultisteprecursionformula;theactualcoefficientsareBrooks'"BetterBeeman"values BETACFFunction "betacf"computesarapidlyconvergentcontinuedfractionneededbyroutine"betai"toevaluatethecumulativeBetadistribution BETAIFunction "betai"evaluatesthecumulativeBetadistributionfunctionastheprobabilitythatarandomvariablefromadistributionwithBetaparameters"a"and"b"willbelessthan"x" BIGBLOCKSubroutine "bigblock"replicatesthecoordinatesofasingleunitcelltogivealargerblockofrepeatedunits BITORSSubroutine "bitors"findsthetotalnumberofbitorsions,pairsofoverlappingdihedralangles,andthenumbersofthefiveatomsdefiningeachbitorsion BMAXFunction


"bmax"computesthemaximumorderoftheBfunctionsneededforevaluationofSlater-type(STO)overlapintegrals BNDERRFunction "bnderr"isthedistancebounderrorfunctionandderivatives;thisversionimplementstheoriginaland Havel's normalized lower bound penalty, the normalized version is preferred when lowerboundsaresmall(aswithNMRNOErestraints),theoriginalpenaltyisneedediflargelowerboundsarepresent BONDSSubroutine "bonds"findsthetotalnumberofcovalentbondsandstorestheatomnumbersoftheatomsdefiningeachbond BORNSubroutine "born"computestheBornradiusofeachatomforusewiththevariousGB/SAsolvationmodels BORN1Subroutine "born1"computesderivativesoftheBornradiiwithrespecttoatomiccoordinatesandincrementstotalenergyderivativesandvirialcomponentsforpotentialsinvolvingBornradii BOUNDSSubroutine "bounds"findsthecenterofmassofeachmoleculeandtranslatesanystraymoleculesbackintotheperiodicbox BSETSubroutine "bset"computesbydownwardrecursiontheBfunctionsusedintheevaluationofSlater-type(STO)overlapintegrals BSPLINESubroutine "bspline"calculatesthecoefficientsforann-thorderB-splineapproximation BSPLINE1Subroutine "bspline1" calculates the coefficients and derivative coefficients for an n-th order B-splineapproximation BSSTEPSubroutine "bsstep" takes a single Bulirsch-Stoer step with monitoring of local truncation error to ensureaccuracy CALENDARSubroutine


"calendar"returnsthecurrenttimeasasetofintegervaluesrepresentingtheyear,month,day,hour,minuteandsecond CELLATOMSubroutine "cellatom"completes theadditionofa symmetryrelatedatomtoaunit cellbyupdating theatomtypeandattachmentarrays CENTERSubroutine "center" moves the weighted centroid of each coordinate set to the origin during least squaressuperposition CERRORSubroutine "cerror"istheerrorhandlingroutinefortheConnollysurfaceareaandvolumecomputation CFFTBSubroutine "cfftb"computesthebackwardcomplexdiscreteFouriertransform,theFouriersynthesis CFFTB1Subroutine CFFTFSubroutine "cfftf"computestheforwardcomplexdiscreteFouriertransform,theFourieranalysis CFFTF1Subroutine CFFTISubroutine "cffti" initializes the array "wsave" which is used in both forward and backward transforms; theprimefactorizationof"n"togetherwithatabulationofthetrigonometricfunctionsarecomputedandstoredin"wsave" CFFTI1Subroutine CHIRERFunction "chirer"computesthechiralityerroranditsderivativeswithrespecttoatomicCartesiancoordinatesasasumthesquaresofdeviationsofchiralvolumesfromtargetvalues CHKCLASHSubroutine "chkclash"determinesifthereareanyatomclasheswhichmightcausetroubleonsubsequentenergyevaluation CHKPOLESubroutine


"chkpole"invertsatomicmultipolemomentsasnecessaryatsiteswithchiral localreferenceframedefinitions CHKRINGSubroutine "chkring" testsangles tobeconstrained for theirpresence in small ringsandremovesconstraintsthatareredundant CHKSIZESubroutine "chksize"computesameasureofoverallglobalstructuralexpansionorcompactionfromthenumberofexcessupperorlowerboundsmatrixviolations CHKTREESubroutine "chktree" tests a minimum energy structure to see if it belongs to the correct progenitor in theexistingmap CHKXYZSubroutine "chkxyz"findsanypairsofatomswithidenticalCartesiancoordinates,andprintsawarningmessage CHOLESKYSubroutine "cholesky"usesamodifiedCholeskymethodtosolvethelinearsystemAx=b,returning"x"in"b";"A"isassumedtobearealsymmetricpositivedefinitematrixwithitsdiagonalanduppertrianglestoredbyrows CIRPLNSubroutine CJKMFunction "cjkm"computesthecoefficientsofsphericalharmonicsexpressedinprolatespheroidalcoordinates CLIMBERSubroutine CLIMBRGDSubroutine CLIMBROTSubroutine CLIMBTORSubroutine CLIMBXYZSubroutine CLOCKSubroutine "clock"determineselapsedCPUtimeinsecondssincethestartofthejob


CLUSTERSubroutine "cluster"getsthepartitioningofthesystemintogroupsandstoresalistofthegrouptowhicheachatombelongs COLUMNSubroutine "column"takestheoff-diagonalHessianelementsstoredassparserowsandsetsupindicestoallowcolumnaccess COMMANDSubroutine "command" uses the standard Unix-like iargc/getarg routines to get the number and values ofargumentsspecifiedonthecommandlineatprogramruntime COMPRESSSubroutine "compress"transfersonlythenon-buriedtorifromthetemporarytoriarraystothefinaltoriarrays CONNECTSubroutine "connect"setsuptheattachedatomarraysstartingfromasetofinternalcoordinates CONNOLLYSubroutine "connolly" uses the algorithms from theAMS/VAMprograms ofMichael Connolly to compute theanalyticalmolecularsurfaceareaandvolumeofacollectionofsphericalatoms;thusit implementsFred Richards'molecular surface definition as a set of analytically defined spherical and toroidalpolygons CONTACTSubroutine "contact"constructsthecontactsurface,cyclesandconvexfaces CONTROLSubroutine "control" gets initial values for parameters that determine the output style and information levelprovidedbyTINKER COORDSSubroutine "coords" converts the three principal eigenvalues/vectors from the metric matrix into atomiccoordinates,andcallsaroutinetocomputethermsdeviationfromthebounds CORRELATEProgram "correlate"computesthetimecorrelationfunctionofsomeuser-suppliedpropertyfromindividualsnapshotframestakenfromamoleculardynamicsorothertrajectory CREATEJVMSubroutine


CREATESERVERSubroutine CREATESYSTEMSubroutine CREATEUPDATESubroutine CRYSTALProgram "crystal"isautilityprogramwhichconvertsbetweenfractionalandCartesiancoordinates,andcangeneratefullunitcellsfromasymmetricunits CUTOFFSSubroutine "cutoffs"initializesandstoressphericalenergycutoffdistancewindows,HessianelementandEwaldsumcutoffs,andthepairwiseneighborgenerationmethod CYTSYSubroutine "cytsy" solvesa systemof linearequations fora cyclically tridiagonal, symmetric,positivedefinitematrix CYTSYPSubroutine "cytsyp" finds the Cholesky factors of a cyclically tridiagonal symmetric, positive definite matrixgivenbytwovectors CYTSYSSubroutine "cytsys"solvesacyclicallytridiagonallinearsystemgiventheCholeskyfactors D1D2Function "d1d2"isautilityfunctionusedincomputationofthereactionfieldrecursivesummationelements DELETESubroutine "delete"removesaspecifiedatomfromtheCartesiancoordinateslistandshiftstheremainingatoms DEPTHFunction DESTROYJVMSubroutine DESTROYSERVERSubroutine DFTMODSubroutine "dftmod" computes the modulus of the discrete Fourier transform of "bsarray", storing it into"bsmod"


DIAGQSubroutine "diagq" is amatrix diagonalization routinewhich is derived from the classical given, housec, andeigenalgorithmswithseveralmodificationstoincreasetheefficiencyandaccuracy DIFFEQSubroutine "diffeq" performs the numerical integration ofan ordinary differentialequation using anadaptivestepsizemethodtosolvethecorrespondingcoupledfirst-orderequationsofthegeneralformdyi/dx=f(x,y1,...,yn)foryi=y1,...,yn DIFFUSEProgram "diffuse"findstheself-diffusionconstantforahomogeneousliquidviatheEinsteinrelationfromasetofstoredmoleculardynamicsframes;molecularcentersofmassareunfoldedandmeansquareddisplacementsarecomputedversustimeseparation DIST2Function "dist2" finds the distance squaredbetween twopoints; used as a service routine by the Connollysurfaceareaandvolumecomputation DISTGEOMProgram "distgeom"usesametricmatrixdistancegeometryproceduretogeneratestructureswithinterpointdistances that lie within specified bounds, with chiral centers that maintain chirality, and withtorsionalanglesrestrainedtodesiredvalues;theuseralsohastheabilitytointeractivelyinspectandalterthetrianglesmoothedboundsmatrixpriortoembedding DMDUMPSubroutine "dmdump"putsthedistancematrixofthefinalstructureintotheupperhalfofamatrix,thedistanceofeachatomtothecentroidonthediagonal,andtheindividualtermsoftheboundserrorsintothelowerhalfofthematrix DOCUMENTProgram "document"generatesaformatteddescriptionofallthecodemodulesorcommonblocks,anindexofroutines called by each source code module, a listing of all valid keywords, a list of include filedependenciesasneededbyaUnix-styleMakefile,oraformattedforcefieldparametersetsummary DOTFunction "dot"findsthedotproductoftwovectors DSTMATSubroutine


"dstmat" selects a distancematrix containing values between the previously smoothedupper andlower bounds; the distance values are chosen fromuniformdistributions, in a triangle correlatedfashion,orusingrandompartialmetrization DYNAMICProgram "dynamic" computes a molecular dynamics trajectory in any of several statistical mechanicalensembleswith optional periodic boundaries and optional coupling to temperature and pressurebathsalternativelyastochasticdynamicstrajectorycanbegenerated EANGANGSubroutine "eangang"calculatestheangle-anglepotentialenergy EANGANG1Subroutine "eangang1"calculatestheangle-anglepotentialenergyandfirstderivativeswithrespecttoCartesiancoordinates EANGANG2Subroutine "eangang2"calculatestheangle-anglepotentialenergysecondderivativeswithrespecttoCartesiancoordinatesusingfinitedifferencemethods EANGANG2ASubroutine "eangang2a" calculates the angle-angle first derivatives for a single interaction with respect toCartesiancoordinates;usedincomputationoffinitedifferencesecondderivatives EANGANG3Subroutine "eangang3"calculatestheangle-anglepotentialenergy;alsopartitionstheenergyamongtheatoms EANGLESubroutine "eangle"calculatestheanglebendingpotentialenergy;projectedin-planeanglesattrigonalcentersorFourieranglebendingtermsareoptionallyused EANGLE1Subroutine "eangle1" calculates the angle bending potential energy and the first derivativeswith respect toCartesiancoordinates;projectedin-planeanglesattrigonalcentersorFourieranglebendingtermsareoptionallyused EANGLE2Subroutine "eangle2"calculatessecondderivativesoftheanglebendingenergyforasingleatomusingamixtureofanalyticalandfinitedifferencemethods;projectedin-planeanglesattrigonalcentersorFourieranglebendingtermsareoptionallyused


EANGLE2ASubroutine "eangle2a" calculates bond angle bending potential energy second derivatives with respect toCartesiancoordinates EANGLE2BSubroutine "eangle2b"computesprojectedin-planebendingfirstderivativesforasingleanglewithrespecttoCartesiancoordinates;usedincomputationoffinitedifferencesecondderivatives EANGLE3Subroutine "eangle3"calculatestheanglebendingpotentialenergy,alsopartitionstheenergyamongtheatoms;projectedin-planeanglesattrigonalcentersorFourieranglebendingtermsareoptionallyused EBONDSubroutine "ebond"calculatesthebondstretchingenergy EBOND1Subroutine "ebond1" calculates the bond stretching energy and first derivatives with respect to Cartesiancoordinates EBOND2Subroutine "ebond2"calculatessecondderivativesofthebondstretchingenergyforasingleatomatatime EBOND3Subroutine "ebond3"calculatesthebondstretchingenergy;alsopartitionstheenergyamongtheatoms EBUCKSubroutine "ebuck"calculatestheBuckinghamexp-6vanderWaalsenergy EBUCK0ASubroutine "ebuck0a"calculatestheBuckinghamexp-6vanderWaalsenergyusingapairwisedoubleloop EBUCK0BSubroutine "ebuck0b" calculates the Buckingham exp-6 van derWaals energy using the method of lights tolocateneighboringatoms EBUCK0CSubroutine "ebuck0c"calculatestheBuckinghamexp-6vanderWaalsenergyviaaGaussianapproximationforpotentialenergysmoothing


EBUCK1Subroutine "ebuck1"calculatestheBuckinghamexp-6vanderWaalsenergyanditsfirstderivativeswithrespecttoCartesiancoordinates EBUCK1ASubroutine "ebuck1a" calculates theBuckinghamexp-6 vanderWaalsenergyand its first derivatives using apairwisedoubleloop EBUCK1BSubroutine "ebuck1b"calculatestheBuckinghamexp-6vanderWaalsenergyanditsfirstderivativesusingthemethodoflightstolocateneighboringatoms EBUCK1CSubroutine "ebuck1c" calculates the Buckingham exp-6 van derWaals energy and its first derivatives via aGaussianapproximationforpotentialenergysmoothing EBUCK2Subroutine "ebuck2"calculatestheBuckinghamexp-6vanderWaalssecondderivativesforasingleatomatatime EBUCK2ASubroutine "ebuck2a"calculates theBuckinghamexp-6vanderWaals secondderivativesusingadouble loopoverrelevantatompairs EBUCK2BSubroutine "ebuck2b" calculates the Buckingham exp-6 van der Waals second derivatives via a Gaussianapproximationforusewithpotentialenergysmoothing EBUCK3Subroutine "ebuck3"calculates theBuckinghamexp-6vanderWaalsenergyandpartitions theenergyamongtheatoms EBUCK3ASubroutine "ebuck3a"calculatestheBuckinghamexp-6vanderWaalsenergyandpartitionstheenergyamongtheatomsusingapairwisedoubleloop EBUCK3BSubroutine "ebuck3b" calculates the Buckingham exp-6 van derWaals energy and also partitions the energyamongtheatomsusingthemethodoflightstolocateneighboringatoms


EBUCK3CSubroutine "ebuck3c"calculatestheBuckinghamexp-6vanderWaalsenergyviaaGaussianapproximationforpotentialenergysmoothing ECHARGESubroutine "echarge"calculatesthecharge-chargeinteractionenergy ECHARGE0ASubroutine "echarge0a"calculatesthecharge-chargeinteractionenergyusingapairwisedoubleloop ECHARGE0BSubroutine "echarge0b" calculates the charge-charge interaction energy using the method of lights to locateneighboringatoms ECHARGE0CSubroutine "echarge0c" calculates the charge-charge interaction energy for use with potential smoothingmethods ECHARGE0DSubroutine "echarge0d"calculatesthecharge-chargeinteractionenergyusingaparticlemeshEwaldsummation ECHARGE0ESubroutine "echarge0e"calculatesthecharge-chargeinteractionenergyusingaparticlemeshEwaldsummationandthemethodoflightstolocateneighboringatoms ECHARGE1Subroutine "echarge1" calculates the charge-charge interaction energy and first derivatives with respect toCartesiancoordinates ECHARGE1ASubroutine "echarge1a" calculates the charge-charge interaction energy and first derivatives with respect toCartesiancoordinatesusingapairwisedoubleloop ECHARGE1BSubroutine "echarge1b" calculates the charge-charge interaction energy and first derivatives with respect toCartesiancoordinatesusingthemethodoflightstolocateneighboringatoms ECHARGE1CSubroutine


"echarge1c" calculates the charge-charge interaction energy and first derivativeswith respect toCartesiancoordinatesforusewithpotentialsmoothingmethods ECHARGE1DSubroutine "echarge1d" calculates the charge-charge interaction energy and first derivatives with respect toCartesiancoordinatesusingaparticlemeshEwaldsummation ECHARGE2Subroutine "echarge2"calculatessecondderivativesofthecharge-chargeinteractionenergyforasingleatom ECHARGE2ASubroutine "echarge2a"calculatessecondderivativesofthecharge-chargeinteractionenergyforasingleatomusingapairwisedoubleloop ECHARGE2BSubroutine "echarge2b"calculatessecondderivativesofthecharge-chargeinteractionenergyforasingleatomforusewithpotentialsmoothingmethods ECHARGE2CSubroutine "echarge2c"calculatessecondderivativesofthecharge-chargeinteractionenergyforasingleatomusingaparticlemeshEwaldsummation ECHARGE3Subroutine "echarge3" calculates the charge-charge interaction energy and partitions the energy among theatoms ECHARGE3ASubroutine "echarge3a" calculates the charge-charge interaction energy and partitions the energy among theatomsusingapairwisedoubleloop ECHARGE3BSubroutine "echarge3b" calculates the charge-charge interaction energy and partitions the energy among theatomsusingthemethodoflightstolocateneighboringatoms ECHARGE3CSubroutine "echarge3c" calculates the charge-charge interaction energy and partitions the energy among theatomsforusewithpotentialsmoothingmethods ECHARGE3DSubroutine


"echarge3d" calculates the charge-charge interaction energy and partitions the energy among theatomsusingaparticlemeshEwaldsummation ECHARGE3ESubroutine "echarge3e" calculates the charge-charge interaction energy and partitions the energy among theatomsusingaparticlemeshEwaldsummationandthemethodoflightstolocateneighboringatoms ECHGDPLSubroutine "echgdpl"calculatesthecharge-dipoleinteractionenergy ECHGDPL1Subroutine "echgdpl1" calculates the charge-dipole interaction energy and first derivatives with respect toCartesiancoordinates ECHGDPL2Subroutine "echgdpl2"calculatessecondderivativesofthecharge-dipoleinteractionenergyforasingleatom ECHGDPL3Subroutine "echgdpl3" calculates the charge-dipole interaction energy; also partitions the energy among theatoms EDIPOLESubroutine "edipole"calculatesthedipole-dipoleinteractionenergy EDIPOLE1Subroutine "edipole1" calculates the dipole-dipole interaction energy and first derivatives with respect toCartesiancoordinates EDIPOLE2Subroutine "edipole2"calculatessecondderivativesofthedipole-dipoleinteractionenergyforasingleatom EDIPOLE3Subroutine "edipole3" calculates the dipole-dipole interaction energy; also partitions the energy among theatoms EGAUSSSubroutine "egauss"calculatestheGaussianexpansionvanderWaalsinteractionenergy


EGAUSS0ASubroutine "egauss0a" calculates the Gaussian expansion van derWaals interaction energy using a pairwisedoubleloop EGAUSS0BSubroutine "egauss0b"calculatestheGaussianexpansionvanderWaalsinteractionenergyforusewithpotentialenergysmoothing EGAUSS1Subroutine "egauss1" calculates the Gaussian expansion van der Waals interaction energy and its firstderivativeswithrespecttoCartesiancoordinates EGAUSS1ASubroutine "egauss1a" calculates the Gaussian expansion van der Waals interaction energy and its firstderivativesusingapairwisedoubleloop EGAUSS1BSubroutine "egauss1b" calculates the Gaussian expansion van der Waals interaction energy and its firstderivativesforusewithstophatpotentialenergysmoothing EGAUSS2Subroutine "egauss2"calculatestheGaussianexpansionvanderWaalssecondderivativesforasingleatomatatime EGAUSS2ASubroutine "egauss2a" calculates the Gaussian expansion van derWaals second derivatives using a pairwisedoubleloop EGAUSS2BSubroutine "egauss2b"calculatestheGaussianexpansionvanderWaalssecondderivativesforstophatpotentialenergysmoothing EGAUSS3Subroutine "egauss3" calculates theGaussian expansion van derWaals interaction energy and partitions theenergyamongtheatoms EGAUSS3ASubroutine "egauss3a"calculates theGaussianexpansion vanderWaals interactionenergy andpartitions theenergyamongtheatomsusingapairwisedoubleloop


EGAUSS3BSubroutine "egauss3b"calculates theGaussianexpansionvanderWaals interactionenergyandpartitions theenergyamongtheatomsusingapairwisedoubleloop EGBSA0ASubroutine "egbsa0a"calculatesthegeneralizedBornpolarizationenergyfortheGB/SAsolvationmodels EGBSA0BSubroutine "egbsa0b"calculates the generalizedBornpolarization energy for theGB/SA solvationmodels forusewithpotentialsmoothingmethodsviaanalogytothesmoothingofCoulomb'slaw EGBSA1ASubroutine "egbsa1a"calculatesthegeneralizedBornenergyandfirstderivativesoftheGB/SAsolvationmodels EGBSA1BSubroutine "egbsa1b"calculatesthegeneralizedBornenergyandfirstderivativesoftheGB/SAsolvationmodelsforusewithpotentialsmoothingmethods EGBSA2ASubroutine "egbsa2a"calculatessecondderivativesofthegeneralizedBornenergytermfortheGB/SAsolvationmodels EGBSA2BSubroutine "egbsa2b"calculatessecondderivativesofthegeneralizedBornenergytermfortheGB/SAsolvationmodelsforusewithpotentialsmoothingmethods EGBSA3ASubroutine "egbsa3a" calculates the generalized Born energy term for the GB/SA solvation models; alsopartitionstheenergyamongtheatoms EGBSA3BSubroutine "egbsa3b"calculates the generalizedBornpolarization energy for theGB/SA solvationmodels forusewithpotentialsmoothingmethodsviaanalogytothesmoothingofCoulomb'slaw;alsopartitionstheenergyamongtheatoms EGEOMSubroutine "egeom"calculatestheenergyduetorestraintsonpositions,distances,anglesandtorsionsaswellasGaussianbasinandsphericaldropletrestraints EGEOM1Subroutine


"egeom1" calculates theenergy and first derivativeswith respect to Cartesian coordinates due torestraintsonpositions,distances,anglesandtorsionsaswellasGaussianbasinandsphericaldropletrestraints EGEOM2Subroutine "egeom2"calculatessecondderivativesofrestraintsonpositions,distances,anglesandtorsionsaswellasGaussianbasinandsphericaldropletrestraints EGEOM3Subroutine "egeom3"calculatestheenergyduetorestraintsonpositions,distances,anglesandtorsionsaswellasGaussianbasinanddropletrestraints;alsopartitionsenergyamongtheatoms EHALSubroutine "ehal"calculatesthebuffered14-7vanderWaalsenergy EHAL0ASubroutine "ehal0a"calculatesthebuffered14-7vanderWaalsenergyusingapairwisedoubleloop EHAL0BSubroutine "ehal0a" calculates the buffered 14-7 van derWaals energy using the method of lights to locateneighboringatoms EHAL1Subroutine "ehal1"calculates thebuffered14-7vanderWaalsenergyand its firstderivativeswith respect toCartesiancoordinates EHAL1ASubroutine "ehal1a"calculatesthebuffered14-7vanderWaalsenergyanditsfirstderivativeswithrespecttoCartesiancoordinatesusingapairwisedoubleloop EHAL1BSubroutine "ehal1b"calculatesthebuffered14-7vanderWaalsenergyanditsfirstderivativeswithrespecttoCartesiancoordinatesusingthemethodoflightstolocateneighboringatoms EHAL2Subroutine "ehal2"calculatesthebuffered14-7vanderWaalssecondderivativesforasingleatomatatime EHAL3Subroutine


"ehal3" calculates the buffered 14-7 van derWaals energy and partitions the energy among theatoms EHAL3ASubroutine "ehal3a" calculates the buffered 14-7 van derWaals energy and partitions the energy among theatomsusingapairwisedoubleloop EHAL3BSubroutine "ehal3b"calculatesthebuffered14-7vanderWaalsenergyandalsopartitionstheenergyamongtheatomsusingthemethodoflightstolocateneighboringatoms EIGENSubroutine "eigen"uses thepowermethod tocompute the largesteigenvaluesandeigenvectorsof themetricmatrix,"valid"issettrueifthefirstthreeeigenvaluesarepositive EIGENRGDSubroutine EIGENROTSubroutine EIGENROTSubroutine EIGENTORSubroutine EIGENXYZSubroutine EIMPROPSubroutine "eimprop"calculatestheimproperdihedralpotentialenergy EIMPROP1Subroutine "eimprop1"calculates improperdihedralenergyand its firstderivativeswith respect toCartesiancoordinates EIMPROP2Subroutine "eimprop2"calculatessecondderivativesoftheimproperdihedralangleenergyforasingleatom EIMPROP3Subroutine "eimprop3" calculates the improper dihedral potential energy; also partitions the energy termsamongtheatoms EIMPTORSubroutine "eimptor"calculatestheimpropertorsionpotentialenergy


EIMPTOR1Subroutine "eimptor1" calculates improper torsion energy and its first derivatives with respect to Cartesiancoordinates EIMPTOR2Subroutine "eimptor2"calculatessecondderivativesoftheimpropertorsionenergyforasingleatom EIMPTOR3Subroutine "eimptor3"calculatestheimpropertorsionpotentialenergy;alsopartitionstheenergytermsamongtheatoms ELJSubroutine "elj"calculatestheLennard-Jones6-12vanderWaalsenergy ELJ0ASubroutine "elj0a"calculatestheLennard-Jones6-12vanderWaalsenergyusingapairwisedoubleloop ELJ0BSubroutine "elj0b"calculatestheLennard-Jones6-12vanderWaalsenergyusingthemethodoflightstolocateneighboringatoms ELJ0CSubroutine "elj0c" calculates the Lennard-Jones 6-12 vanderWaals energy viaaGaussian approximation forpotentialenergysmoothing ELJ0DSubroutine "elj0d"calculatestheLennard-Jones6-12vanderWaalsenergyforusewithstophatpotentialenergysmoothing ELJ1Subroutine "elj1"calculatestheLennard-Jones6-12vanderWaalsenergyanditsfirstderivativeswithrespecttoCartesiancoordinates ELJ1ASubroutine "elj1a" calculates the Lennard-Jones 6-12 van derWaals energy and its first derivatives using apairwisedoubleloop ELJ1BSubroutine


"elj1b" calculates the Lennard-Jones 6-12 vanderWaals energyand its first derivatives using themethodoflightstolocateneighboringatoms ELJ1CSubroutine "elj1c" calculates the Lennard-Jones 6-12 van der Waals energy and its first derivatives via aGaussianapproximationforpotentialenergysmoothing ELJ1DSubroutine "elj1d"calculatesthevanderWaalsinteractionenergyanditsfirstderivativesforusewithstophatpotentialenergysmoothing ELJ2Subroutine "elj2"calculatestheLennard-Jones6-12vanderWaalssecondderivativesforasingleatomatatime ELJ2ASubroutine "elj2a"calculatestheLennard-Jones6-12vanderWaalssecondderivativesusingadoubleloopoverrelevantatompairs ELJ2BSubroutine "elj2b" calculates the Lennard-Jones 6-12 van der Waals second derivatives via a Gaussianapproximationforusewithpotentialenergysmoothing ELJ2CSubroutine "elj2c" calculates the Lennard-Jones 6-12 van derWaals second derivatives for usewith stophatpotentialenergysmoothing ELJ3Subroutine "elj3"calculatestheLennard-Jones6-12vanderWaalsenergyandalsopartitionstheenergyamongtheatoms ELJ3ASubroutine "elj3a"calculatestheLennard-Jones6-12vanderWaalsenergyandalsopartitionstheenergyamongtheatomsusingapairwisedoubleloop ELJ3BSubroutine "elj3b"calculatestheLennard-Jones6-12vanderWaalsenergyandalsopartitionstheenergyamongtheatomsusingthemethodoflightstolocateneighboringatoms ELJ3CSubroutine


"elj3c"calculatestheLennard-Jones6-12vanderWaalsenergyandalsopartitionstheenergyamongtheatomsviaaGaussianapproximationforpotentialenergysmoothing ELJ3DSubroutine "elj3d"calculatestheLennard-Jones6-12vanderWaalsenergyandalsopartitionstheenergyamongtheatomsforusewithstophatpotentialenergysmoothing EMBEDSubroutine "embed"isadistancegeometryroutinepatternedaftertheideasofGordonCrippen,IrwinKuntzandTimHavel; it takesas inputa setofupperand lowerboundson the interpointdistances, chiralityrestraintsandtorsionalrestraints,andattemptstogenerateasetofcoordinatesthatsatisfytheinputboundsandrestraints EMETALSubroutine "emetal"calculatesthetransitionmetalligandfieldenergy EMETAL1Subroutine "emetal1"calculatesthetransitionmetalligandfieldenergyanditsfirstderivativeswithrespecttoCartesiancoordinates EMETAL2Subroutine "emetal2"calculatesthetransitionmetalligandfieldsecondderivativesforasingleatomatatime EMETAL3Subroutine "emetal3"calculatesthetransitionmetalligandfieldenergyandalsopartitionstheenergyamongtheatoms EMM3HBSubroutine "emm3hb" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogenbondingenergy EMM3HB0ASubroutine "emm3hb0a" calculates the MM3 exp-6 van derWaals and directional charge transfer hydrogenbondingenergyusingapairwisedoubleloop EMM3HB0BSubroutine "emm3hb0b" calculates the MM3 exp-6 van derWaals and directional charge transfer hydrogenbondingenergyusingthemethodoflightstolocateneighboringatoms EMM3HB1Subroutine


"emm3hb1" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogenbondingenergywithrespecttoCartesiancoordinates EMM3HB1ASubroutine "emm3hb1a" calculates the MM3 exp-6 van derWaals and directional charge transfer hydrogenbondingenergywithrespecttoCartesiancoordinatesusingapairwisedoubleloop EMM3HB1BSubroutine "emm3hb1b" calculates the MM3 exp-6 van derWaals and directional charge transfer hydrogenbonding energy with respect to Cartesian coordinates using the method of lights to locateneighboringatoms EMM3HB2Subroutine "emm3hb2" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogenbondingsecondderivativesforasingleatomatatime EMM3HB3Subroutine "emm3hb3" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogenbondingenergy,andpartitionstheenergyamongtheatoms EMM3HB3ASubroutine "emm3hb3" calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogenbondingenergy,andpartitionstheenergyamongtheatoms EMM3HB3BSubroutine "emm3hb3b" calculates the MM3 exp-6 van derWaals and directional charge transfer hydrogenbondingenergyusingthemethodoflightstolocateneighboringatoms EMPOLESubroutine "empole" calculates the electrostatic energy due to atomic multipole interactions and dipolepolarizability EMPOLE0ASubroutine "empole0a" calculates the electrostatic energy due to atomic multipole interactions and dipolepolarizabilityusingapairwisedoubleloop EMPOLE0BSubroutine "empole0b" calculates the electrostatic energy due to atomic multipole interactions and dipolepolarizabilityusingaregularEwaldsummation


EMPOLE1Subroutine "empole1" calculates themultipoleanddipole polarization energyandderivativeswith respect toCartesiancoordinates EMPOLE1ASubroutine "empole1a"calculatesthemultipoleanddipolepolarizationenergyandderivativeswithrespecttoCartesiancoordinatesusingapairwisedoubleloop EMPOLE1BSubroutine "empole1b"calculatesthemultipoleanddipolepolarizationenergyandderivativeswithrespecttoCartesiancoordinatesusingaregularEwaldsummation EMPOLE2Subroutine "empole2"calculatessecondderivativesofthemultipoleanddipolepolarizationenergyforasingleatomatatime EMPOLE2ASubroutine "empole2a" computes multipole and dipole polarization first derivatives for a single atom withrespecttoCartesiancoordinates;usedtogetfinitedifferencesecondderivatives EMPOLE3Subroutine "empole3" calculates the electrostatic energy due to atomic multipole interactions and dipolepolarizability,andpartitionstheenergyamongtheatoms EMPOLE3ASubroutine "empole3a" calculates the electrostatic energy due to atomic multipole interactions and dipolepolarizability,andpartitionstheenergyamongtheatomsusingadoubleloop EMPOLE3BSubroutine "empole3b" calculates the electrostatic energy due to atomic multipole interactions and dipolepolarizability,andpartitionstheenergyamongtheatomsusingaregularEwaldsummation ENERGYFunction "energy"callsthesubroutinestocalculatethepotentialenergytermsandsumsuptoformthetotalenergy ENRGYZESubroutine "energyze" isan auxiliary routine for the analyze program that performs the energy analysis andprintsthetotalandintermolecularenergies


EOPBENDSubroutine "eopbend"computestheout-of-planebendpotentialenergyattrigonalcentersviaaWilson-Decius-Crossanglebend EOPBEND1Subroutine "eopbend1"computestheout-of-planebendpotentialenergyandfirstderivativesattrigonalcentersviaaWilson-Decius-Crossanglebend EOPBEND2Subroutine "eopbend2"calculatessecondderivativesoftheout-of-planebendenergyviaaWilson-Decius-Crossanglebendforasingleatomusingfinitedifferencemethods EOPBEND2ASubroutine "eopbend2a" calculates out-of-plane bending first derivatives at a trigonal center via a Wilson-Decius-Crossanglebend;usedincomputationoffinitedifferencesecondderivatives EOPBEND3Subroutine "eopbend3"computestheout-of-planebendpotentialenergyattrigonalcentersviaaWilson-Decius-Crossanglebend;alsopartitionstheenergyamongtheatoms EOPDISTSubroutine "eopdist" computes the out-of-plane distance potential energy at trigonal centers via the centralatomheight EOPDIST1Subroutine "eopdist1" computes the out-of-plane distance potential energy and first derivatives at trigonalcentersviathecentralatomheight EOPDIST2Subroutine "eopdist2"calculatessecondderivativesoftheout-of-planedistanceenergyforasingleatomviathecentralatomheight EOPDIST3Subroutine "eopdist3" computes the out-of-plane distance potential energy at trigonal centers via the centralatomheight;alsopartitionstheenergyamongtheatoms EPITORSSubroutine "epitors"calculatesthepi-orbitaltorsionpotentialenergy EPITORS1Subroutine


"epitors1" calculates the pi-orbital torsion potential energy and first derivatives with respect toCartesiancoordinates EPITORS2Subroutine "epitors2"calculatesthesecondderivativesofthepi-orbitaltorsionenergyforasingleatomusingfinitedifferencemethods EPITORS2ASubroutine "epitors2a"calculatesthepi-orbitaltorsionfirstderivatives;usedincomputationoffinitedifferencesecondderivatives EPITORS3Subroutine "epitors3"calculatesthepi-orbitaltorsionpotentialenergy;alsopartitionstheenergytermsamongtheatoms EPMESubroutine "epme" computes the reciprocal space energy for a particlemesh Ewald summation over partialcharges EPME1Subroutine "epme1" computes the reciprocal space energy and first derivatives for a particle mesh Ewaldsummation EPME3Subroutine "epme3" computes the reciprocal spaceenergy for a particlemeshEwald summation over partialchargesandprintsinformationabouttheenergyoverthechargegridpoints EPUCLCSubroutine EREALSubroutine "ereal" evaluates the real space portion of the regular Ewald summation energy due to atomicmultipoleinteractionsanddipolepolarizability EREAL1Subroutine "ereal1"evaluatestherealspaceportionoftheregularEwaldsummationenergyandgradientduetoatomicmultipoleinteractionsanddipolepolarizability EREAL3Subroutine "ereal3" evaluates the real space portion of the regular Ewald summation energy due to atomicmultipoleinteractionsanddipolepolarizabilityandpartitionstheenergyamongtheatoms


ERECIPSubroutine "erecip"evaluatesthereciprocalspaceportionoftheregularEwaldsummationenergyduetoatomicmultipoleinteractionsanddipolepolarizability ERECIP1Subroutine "erecip1" evaluates the reciprocal space portion of the regular Ewald summation energy andgradientduetoatomicmultipoleinteractionsanddipolepolarizability ERECIP3Subroutine "erecip3" evaluates the reciprocal space portion of the regular Ewald summation energy due toatomicmultipoleinteractionsanddipolepolarizability,andprintsinformationabouttheenergyoverthereciprocallatticevectors ERFFunction "erf" computes a numerical approximation to the value of the error function via a Chebyshevapproximation ERFCFunction "erfc"computesanumericalapproximationtothevalueofthecomplementaryerrorfunctionviaaChebyshevapproximation ERFCORESubroutine "erfcore"evaluateserf(x)orerfc(x)forarealargumentx;whencalledwithmodesetto0itreturnserf,amodeof1returnserfc;usesrationalfunctionsthatapproximateerf(x)anderfc(x)toatleast18significantdecimaldigits ERFIKSubroutine "erfik"computethereactionfieldenergyduetoasinglepairofatomicmultipoles ERFINVFunction "erfinv"evaluatestheinverseoftheerrorfunctionerfforarealargumentintherange(-1,1)usingarationalfunctionapproximationfollowedbycyclesofNewton-Raphsoncorrection ERXNFLDSubroutine "erxnfld"calculatesthemacroscopicreactionfieldenergyarisingfromasetofatomicmultipoles ERXNFLD1Subroutine "erxnfld1"calculatesthemacroscopicreactionfieldenergyandderivativeswithrespecttoCartesiancoordinates


ERXNFLD2Subroutine "erxnfld2"calculatessecondderivativesofthemacroscopicreactionfieldenergyforasingleatomatatime ERXNFLD3Subroutine "erxnfld3"calculatesthemacroscopicreactionfieldenergy,andalsopartitionstheenergyamongtheatoms ESOLVSubroutine "esolv" calculates the continuum solvation energy via either theEisenberg-McLachlanASPmodel,Ooi-ScheragaSASAmodel,variousGB/SAmethodsortheACEmodel ESOLV1Subroutine "esolv1" calculates thecontinuum solvation energy and first derivativeswith respect to Cartesiancoordinates using either the Eisenberg-McLachlan ASP, Ooi-Scheraga SASA or various GB/SAsolvationmodels ESOLV2Subroutine "esolv2"calculatessecondderivativesofthecontinuumsolvationenergyusingeithertheEisenberg-McLachlanASP,Ooi-ScheragaSASAorvariousGB/SAsolvationmodels ESOLV3Subroutine "esolv3"calculatesthecontinuumsolvationenergyusingeithertheEisenberg-McLachlanASPmodel,Ooi-Scheraga SASA model, various GB/SA methods or the ACE model; also partitions the energyamongtheatoms ESTRBNDSubroutine "estrbnd"calculatesthestretch-bendpotentialenergy ESTRBND1Subroutine "estrbnd1" calculates the stretch-bend potential energy and first derivatives with respect toCartesiancoordinates ESTRBND2Subroutine "estrbnd2"calculatesthestretch-bendpotentialenergysecondderivativeswithrespecttoCartesiancoordinates ESTRBND3Subroutine "estrbnd3"calculatesthestretch-bendpotentialenergy;alsopartitionstheenergyamongtheatoms


ESTRTORSubroutine "estrtor"calculatesthestretch-torsionpotentialenergy ESTRTOR1Subroutine "estrtor1" calculates the stretch-torsion energy and first derivatives with respect to Cartesiancoordinates ESTRTOR2Subroutine "estrtor2" calculates the stretch-torsion potential energy second derivatives with respect toCartesiancoordinates ESTRTOR3Subroutine "estrtor3"calculatesthestretch-torsionpotentialenergy;alsopartitionstheenergytermsamongtheatoms ETORSSubroutine "etors"calculatesthetorsionalpotentialenergy ETORS0ASubroutine "etors0a"calculatesthetorsionalpotentialenergyusingastandardsumofFourierterms ETORS0BSubroutine "etors0b"calculatesthetorsionalpotentialenergyforusewithpotentialenergysmoothingmethods ETORS1Subroutine "etors1" calculates the torsional potential energy and first derivatives with respect to Cartesiancoordinates ETORS1ASubroutine "etors1a" calculates the torsional potential energy and first derivativeswith respect to CartesiancoordinatesusingastandardsumofFourierterms ETORS1BSubroutine "etors1b" calculates the torsional potential energy and first derivativeswith respect to Cartesiancoordinatesforusewithpotentialenergysmoothingmethods ETORS2Subroutine


"etors2"calculatesthesecondderivativesofthetorsionalenergyforasingleatom ETORS2ASubroutine "etors2a"calculatesthesecondderivativesofthetorsionalenergyforasingleatomusingastandardsumofFourierterms ETORS2BSubroutine "etors2b" calculates the second derivatives of the torsional energy for a single atom for usewithpotentialenergysmoothingmethods ETORS3Subroutine "etors3"calculatesthetorsionalpotentialenergy;alsopartitionstheenergyamongtheatoms ETORS3ASubroutine "etors3a" calculates the torsional potential energy using a standard sum of Fourier terms andpartitionstheenergyamongtheatoms ETORS3BSubroutine "etors3b"calculatesthetorsionalpotentialenergyforusewithpotentialenergysmoothingmethodsandpartitionstheenergyamongtheatoms ETORTORSubroutine "etortor"calculatesthetorsion-torsionpotentialenergy ETORTOR1Subroutine "etortor1" calculates the torsion-torsion energy and first derivatives with respect to Cartesiancoordinates ETORTOR2Subroutine "etortor2" calculates the torsion-torsion potential energy second derivatives with respect toCartesiancoordinates ETORTOR3Subroutine "etortor3" calculates the torsion-torsionpotential energy; also partitions theenergy termsamongtheatoms EUREYSubroutine "eurey"calculatestheUrey-Bradley1-3interactionenergy


EUREY1Subroutine "eurey1" calculates the Urey-Bradley interaction energy and its first derivatives with respect toCartesiancoordinates EUREY2Subroutine "eurey2"calculatessecondderivativesoftheUrey-Bradleyinteractionenergyforasingleatomatatime EUREY3Subroutine "eurey3"calculatestheUrey-Bradleyenergy;alsopartitionstheenergyamongtheatoms EWALDCOFSubroutine "ewaldcof" finds a value of the Ewald coefficient such that all terms beyond the specified cutoffdistancewillhaveanvaluelessthanaspecifiedtolerance EXPLORESubroutine "explore" uses simulated annealing on an initial crude embedded distance geoemtry structure torefineversusthebound,chirality,planarityandtorsionalerrorfunctions EXTRASubroutine "extra"calculatesanyadditionaluserdefinedpotentialenergycontribution EXTRA1Subroutine "extra1"calculatesanyadditionaluserdefinedpotentialenergycontributionanditsfirstderivatives EXTRA2Subroutine "extra2"calculatessecondderivativesofanyadditionaluserdefinedpotentialenergycontributionforasingleatomatatime EXTRA3Subroutine "extra3"calculatesanyadditionaluserdefinedpotentialcontributionandalsopartitionstheenergyamongtheatoms FATALSubroutine "fatal" terminates execution due to a user request, a severe error or some other nonstandardcondition FFTBACKSubroutine


FFTFRONTSubroutine FFTSETUPSubroutine FIELDSubroutine "field" sets the force field potential energy functions from a parameter file and modificationsspecifiedinakeyfile FINALSubroutine "final"performsanyfinalprogramactions,printsastatusmessage,andthenpausesifnecessarytoavoidclosingtheexecutionwindow FINDATMSubroutine "findatm"locatesaspecificPDBatomnametypewithinarangeofatomsfromthePDBfile,returnszeroifthenametypewasnotfound FIXPDBSubroutine "fixpdb"correctsproblemswithPDBfilesbyconvertingresidueandatomnamestotheformsusedbyTINKER FRACDISTSubroutine "fracdist" computes a normalized distribution of the pairwise fractional distances between thesmoothedupperandlowerbounds FREEUNITFunction "freeunit"findsanunopenedFortranI/Ounitandreturnsitsnumericalvaluefrom1to99;theunitsalreadyassignedto"input"and"iout"(usually5and6)areskippedsincetheyhavespecialmeaningasthedefaultI/Ounits GAMMLNFunction "gammln"usesa seriesexpansiondue toLanczos tocompute thenatural logarithmof theGammafunctionat"x"in[0,1] GDAProgram "gda"implementsGaussianDensityAnnealing(GDA)algorithmforglobaloptimizationviasimulatedannealing GDA1Subroutine GDA2Function GDA3Subroutine


GDASTATSubroutine GENDOTSubroutine "gendot" finds thecoordinatesofa specifiednumberof surfacepoints fora spherewith the inputradiusandcoordinatecenter GEODESICSubroutine "geodesic"smoothstheupperandlowerdistanceboundsviathetriangleinequalityusingasparsematrixversionofashortestpathalgorithm GEOMETRYFunction "geometry"findsthevalueoftheinteratomicdistance,angleordihedralangledefinedbytwotofourinputatoms GETBASESubroutine "getbase" finds the base heavy atoms for a single nucleotide residue and copies the names andcoordinatestotheProteinDataBankfile GETIMESubroutine "getime"getselapsedCPUtimeinsecondsforaninterval GETINTSubroutine "getint"asksforaninternalcoordinatefilename,thenreadstheinternalcoordinatesandcomputesCartesiancoordinates GETKEYSubroutine "getkey" finds a valid keyfile and stores its contents as line images for subsequent keywordparametersearching GETMOL2Subroutine "getmol2"asksforaSybylMOL2moleculefilename,thenreadsthecoordinatesfromthefile GETMONITORSubroutine GETNUCHSubroutine "getnuch" finds the nucleotide hydrogen atoms for a single residue and copies the names andcoordinatestotheProteinDataBankfile GETNUMBSubroutine


"getnumb" searchsan input string from left to right for an integer andputs the numeric value in"number";returnszerowith"next"unchangedifnointegervalueisfound GETPDBSubroutine "getpdb"asksforaProteinDataBankfilename,thenreadsinthecoordinatesfile GETPRBSubroutine "getprb"testsforapossibleprobepositionattheinterfacebetweenthreeneighboringatoms GETPRMSubroutine "getprm"findsthepotentialenergyparameterfileandthenopensandreadstheparameters GETPROHSubroutine "getproh" finds the hydrogen atoms for a single amino acid residue and copies the names andcoordinatestotheProteinDataBankfile GETREFSubroutine "getref" copies structure information from the reference area into the standard variables for thecurrentsystemstructure GETSEQSubroutine "getseq"asks the user for the amino acid sequence and torsional angle values needed to define apeptide GETSEQNSubroutine "getseqn"asks theuser for thenucleotidesequenceand torsionalanglevaluesneeded todefineanucleicacid GETSIDESubroutine "getside"findsthesidechainheavyatomsforasingleaminoacidresidueandcopiesthenamesandcoordinatestotheProteinDataBankfile GETSTRINGSubroutine "getstring"searchsforaquotedtextstringwithinaninputcharacterstring;theregionbetweenthefirstandsecondquotes is returnedas the"text"; if theactual text is too long,only thefirstpart isreturned GETTEXTSubroutine


"gettext"searchsaninputstringforthefirststringofnon-blankcharacters;theregionfromanon-blankcharactertothefirstblankspaceisreturnedas"text";iftheactualtextistoolong,onlythefirstpartisreturned GETTORSubroutine "gettor"testsforapossibletoruspositionattheinterfacebetweentwoatoms,andfindsthetorusradius,centerandaxis GETWORDSubroutine "getword"searchsaninputstringforthefirstalphabeticcharacter(A-Zora-z);theregionfromthisfirst character to the firstblankspaceorcomma is returnedasa "word"; if theactualword is toolong,onlythefirstpartisreturned GETXYZSubroutine "getxyz"asksforaCartesiancoordinatefilename,thenreadsinthecoordinatesfile GRADIENTSubroutine "gradient" calls subroutines to calculate the potential energy and first derivativeswith respect toCartesiancoordinates GRADRGDSubroutine "gradrgd" calls subroutines to calculate the potential energy and first derivativeswith respect torigidbodycoordinates GRADROTSubroutine "gradrot"callssubroutinestocalculatethepotentialenergyanditstorsionalfirstderivatives GRAFICSubroutine "grafic"outputstheupper&lowertrianglesanddiagonalofasquarematrixinaschematicformforvisualinspection GROUPSSubroutine "groups"testsasetofatomstoseeifallaremembersofasingleatomgrouporapairofatomgroups;ifso,thenthecorrectintra-orintergroupweightisassigned GRPLINESubroutine "grpline"testseachatomgroupforlinearityofthesitescontainedinthegroup GYRATESubroutine "gyrate"computestheradiusofgyrationofamolecularsystemfromitsatomiccoordinates


HANGLESubroutine "hangle"constructshybridanglebendingparametersgivenaninitialstate,finalstateand"lambda"value HATOMSubroutine "hatom"assignsanewatomtypetoeachhybridsite HBONDSubroutine "hbond"constructshybridbondstretchparametersgivenan initial state, final stateand"lambda"value HCHARGESubroutine "hcharge" constructs hybrid charge interaction parameters given an initial state, final state and"lambda"value HDIPOLESubroutine "hdipole" constructs hybrid dipole interaction parameters given an initial state, final state and"lambda"value HESSIANSubroutine "hessian"callssubroutinestocalculatetheHessianelementsforeachatominturnwithrespecttoCartesiancoordinates HESSRGDSubroutine "hessrgd" computes the numerical Hessian elements with respect to rigid body coordinates via6*ngroup+1gradientevaluations HESSROTSubroutine "hessrot"computesthenumericalHessianelementswithrespecttotorsionalangles;eitherthefullmatrixor justthediagonalcanbecalculated;thefullmatrixneedsnomega+1gradientevaluationswhilethediagonalrequiresjusttwogradientcalls HIMPTORSubroutine "himptor" constructs hybrid improper torsional parameters given an initial state, final state and"lambda"value HSTRBNDSubroutine "hstrbnd"constructshybridstretch-bendparametersgivenaninitialstate,finalstateand"lambda"value


HSTRTORSubroutine "hstrtor"constructshybridstretch-torsionparametersgivenaninitialstate,finalstateand"lambda"value HTORSSubroutine "htors"constructshybridtorsionalparametersforagiveninitialstate,finalstateand"lambda"value HVDWSubroutine "hvdw"constructshybridvanderWaalsparametersgivenaninitialstate,finalstateand"lambda"value HYBRIDSubroutine "hybrid" constructs the hybrid hamiltonian for a specified initial state, final state and mutationparameter"lambda" IJKPTSSubroutine "ijkpts"storesasetofindicesusedduringcalculationofmacroscopicreactionfieldenergetics IMAGESubroutine "image"takesthecomponentsofpairwisedistancebetweentwopointsinthesameorneighboringperiodicboxesandconvertstothecomponentsoftheminimumimagedistance IMPOSESubroutine "impose" performs the least squares best superposition of two atomic coordinate sets via aquaternion method; upon return, the first coordinate set is unchanged while the second set istranslatedandrotatedtogivebestfit;thefinalrootmeansquarefitisreturnedin"rmsvalue" INDUCESubroutine "induce" computes the induced dipole moment at each polarizable site due to direct or mutualpolarization; assumes that multipole components have already been rotated into the globalcoordinateframe INDUCE0ASubroutine "induce0a"computes the induceddipolemoment at eachpolarizable site using a pairwise doubleloop INDUCE0BSubroutine "induce0b" computes the induced dipole moment at each polarizable site using a regular Ewaldsummation


INEDGESubroutine "inedge"insertsaconcaveedgeintothelinkedlistforitstemporarytorus INERTIASubroutine "inertia" computes the principalmoments of inertia for the system, and optionally translates thecenterofmasstotheoriginandrotatestheprincipalaxesontotheglobalaxes INITERRFunction "initerr"istheinitialerrorfunctionandderivativesforadistancegeometryembedding;itincludescomponentsfromthelocalgeometryandtorsionalrestrainterrors INITIALSubroutine "initial" sets up original values for some parameters and variables that might not otherwise getinitialized INITPRMSubroutine "initprm"completelyinitializesaforcefieldbysettingallparameterstozeroandusingdefaultsforcontrolvalues INITRESSubroutine "initres" sets names for biopolymer residue types used in PDB file conversion and automatedgenerationofstructures INITROTSubroutine "initrot" sets the torsional angleswhich are to be rotated in subsequent computation, by defaultautomatically selects all rotatable single bonds; assumes internal coordinates have already beensetup INSERTSubroutine "insert"addsthespecifiedatomtotheCartesiancoordinateslistandshiftstheremainingatoms INTEDITProgram "intedit" allows the user to extract information from or alter the values within an internalcoordinatesfile INTXYZProgram "intxyz" takes as input an internal coordinates file, converts to and then writes out Cartesiancoordinates


INVBETAFunction "invbeta"computestheinverseBetadistributionfunctionviaacombinationofNewtoniterationandbisectionsearch INVERTSubroutine "invert"invertsamatrixusingtheGauss-Jordanmethod IPEDGESubroutine "ipedge"insertsconvexedgeintolinkedlistforatom ISPLPESubroutine "isplpe"computesthecoefficientsforacubicperiodicinterpolatingspline JACOBISubroutine "jacobi" performs a matrix diagonalization of a real symmetric matrix by the method of Jacobirotations KANGANGSubroutine "kangang" assigns the parameters for angle-angle cross term interactions and processes new orchangedparametervalues KANGLESubroutine "kangle" assigns the force constants and ideal angles for the bond angles; also processes new orchangedparameters KATOMSubroutine "katom"assignsanatomtypedefinitions toeachatomin thestructureandprocessesanyneworchangedvalues KBONDSubroutine "kbond"assignsaforceconstantandidealbondlengthtoeachbondinthestructureandprocessesanyneworchangedparametervalues KCHARGESubroutine "kcharge" assigns partial charges to the atoms within the structure and processes any new orchangedvalues KCHIRALSubroutine


"kchiral"determinesthetargetvalueforeachchiralityandplanarityrestraintasthesignedvolumeoftheparallelpipedspannedbyvectorsfromacommonatomtoeachofthreeotheratoms KDIPOLESubroutine "kdipole"assignsbonddipolestothebondswithinthestructureandprocessesanyneworchangedvalues KENEGSubroutine "keneg"appliesprimaryandsecondaryelectronegativitybondlengthcorrectionstoapplicablebondparameters KEWALDSubroutine "kewald"assignsbothregularEwaldsummationandparticlemeshEwaldparametersforaperiodicbox KGEOMSubroutine "kgeom" asisgns parameters for geometric restraint terms to be included in the potential energycalculation KIMPROPSubroutine "kimprop" assigns potential parameters to each improper dihedral in the structure andprocessesanychangedvalues KIMPTORSubroutine "kimptor"assignstorsionalparameterstoeachimpropertorsioninthestructureandprocessesanychangedvalues KINETICSubroutine "kinetic"computesthetotalkineticenergyandkineticenergycontributionstothepressuretensorbysummingovervelocities KMETALSubroutine "kmetal" assigns ligand field parameters to transition metal atoms and processes any new orchangedparametervalues KMPOLESubroutine "kmpole"assignsatomicmultipolemomentstotheatomsofthestructureandprocessesanyneworchangedvalues KOPBENDSubroutine


"kopbend"assignstheforceconstantsforout-of-planebendingattrigonalcentersviaWilson-Decius-Crossanglebends;alsoprocessesanyneworchangedparametervalues KOPDISTSubroutine "kopdist"assignstheforceconstantsforout-of-planedistanceattrigonalcentersviathecentralatomheight;alsoprocessesanyneworchangedparametervalues KORBITSubroutine "korbit" assigns pi-orbital parameters to conjugated systems and processes any new or changedparameters KPITORSSubroutine "kpitors"assignspi-orbitaltorsionparameterstotorsionsneedingthem,andprocessesanyneworchangedvalues KPOLARSubroutine "kpolar"assignsatomicdipolepolarizabilitiestotheatomswithinthestructureandprocessesanyneworchangedvalues KSOLVSubroutine "ksolv" assigns continuum solvation energy parameters for the Eisenberg-McLachlan ASP, Ooi-ScheragaSASAorvariousGB/SAsolvationmodels KSTRBNDSubroutine "kstrbnd"assigns the parameters for the stretch-bend interactions andprocesses newor changedparametervalues KSTRTORSubroutine "kstrtor" assigns stretch-torsion parameters to torsions needing them, and processes any new orchangedvalues KTORSSubroutine "ktors" assigns torsional parameters to each torsion in the structure and processes any new orchangedvalues KTORTORSubroutine "ktortor" assigns torsion-torsion parameters to adjacent torsion pairs and processes any new orchangedvalues KUREYSubroutine


"kurey"assigns the forceconstantsand idealdistancesfor theUrey-Bradley1-3 interactions;alsoprocessesanyneworchangedparametervalues KVDWSubroutine "kvdw"assignstheparameterstobeusedincomputingthevanderWaalsinteractionsandprocessesanyneworchangedvaluesfortheseparameters LATTICESubroutine "lattice"storestheperiodicboxdimensionsandsetsanglevaluestobeusedincomputingfractionalcoordinates LBFGSSubroutine "lbfgs"isalimitedmemoryBFGSquasi-newtonnonlinearoptimizationroutine LIGASESubroutine "ligase"translatesanucleicacidstructureinProteinDataBankformattoaCartesiancoordinatefileandsequencefile LIGHTSSubroutine "lights"computesthesetofnearestneighborinteractionsusingthemethodoflightsalgorithm LINBODYSubroutine "linbody" finds the angular velocity of a linear rigid body given the inertia tensor and angularmomentum LMSTEPSubroutine "lmstep"computestheLevenberg-Marquardtstepduringanonlinearleastsquarescalculation;thisversion is based upon ideas from the Minpack routine LMPAR together with with the internaldoublingstrategyofDennisandSchnabel LOCALMINSubroutine "localmin" is used during normal mode local search to perform a Cartesian coordinate energyminimization LOCALRGDSubroutine "localrgd"isusedduringthePSSlocalsearchproceduretoperformarigidbodyenergyminimization LOCALROTSubroutine


"localrot" is used during the PSS local search procedure to perform a torsional space energyminimization LOCALXYZSubroutine "localxyz" is used during the potential smoothing and search procedure to perform a localoptimizationatthecurrentsmoothinglevel LOCERRFunction "locerr"isthelocalgeometryerrorfunctionandderivativesincludingthe1-2,1-3and1-4distanceboundrestraints LOWCASESubroutine "lowcase"convertsatextstringtoalllowercaseletters MAJORIZESubroutine "majorize" refines the projected coordinates by attempting tominimize the least square residualbetweenthetrialdistancematrixandthedistancescomputedfromthecoordinates MAKEINTSubroutine "makeint" converts Cartesian to internal coordinates where selection of internal coordinates iscontrolledby"mode" MAKEPDBSubroutine "makexyz"convertsasetofCartesiancoordinatestoProteinDataBankformatwithspecialhandlingforsystemsconsistingofpolypeptidechains,ligandsandwatermolecules MAKEREFSubroutine "makeref" copies the information contained in the "xyz" file of the current structure intocorrespondingreferenceareas MAKEXYZSubroutine "makexyz"generatesa completesetofCartesiancoordinates fora full structure fromthe internalcoordinatevalues MAPCHECKSubroutine "mapcheck"checksthecurrentminimumenergystructureforpossibleadditiontothemasterlistoflocalminima MAXWELLFunction


"maxwell" returns a speed in Angstroms/picosecond randomly selected from a 3-D Maxwell-Boltzmanndistributionforthespecifiedparticlemassandsystemtemperature MCM1Function "mcm1" is a service routine that computes the energy and gradient for truncated NewtonoptimizationinCartesiancoordinatespace MCM2Subroutine "mcm2"isaserviceroutinethatcomputesthesparsematrixHessianelementsfortruncatedNewtonoptimizationinCartesiancoordinatespace MCMSTEPFunction "mcmstep"implementstheminimizationphaseofanMCMstepviaCartesianminimizationfollowingaMonteCarlostep MDINITSubroutine "mdinit" initializes the velocities and accelerations for amolecular dynamics trajectory, includingrestarts MDRESTSubroutine "mdrest" finds and removes any translational or rotational kinetic energy of the overall systemcenterofmass MDSAVESubroutine "mdsave" writes molecular dynamics trajectory snapshots and auxiliary files with velocity andinduceddipoleinformation;alsochecksforuserrequestedterminationofasimulation MDSTATSubroutine "mdstat"iscalledateachmoleculardynamicstimesteptoformstatisticsonvariousaveragevaluesandfluctuations,andtoperiodicallysavethestateofthetrajectory MEASFNSubroutine MEASFPSubroutine MEASFSSubroutine MEASPMSubroutine "measpm"computesthevolumeofasingleprismsectionofthefullinteriorpolyhedron MECHANICSubroutine


"mechanic"setsupneededparametersforthepotentialenergycalculationandreadsinmanyoftheuserselectableoptions MERGESubroutine "merge" combines the reference and current structures into a single new "current" structurecontainingthereferenceatomsfollowedbytheatomsofthecurrentstructure METRICSubroutine "metric"takesasinputthetrialdistancematrixandcomputesthemetricmatrixofallpossibledotproducts between the atomic vectors and the center of mass using the law of cosines and thefollowingformulaforthedistancestothecenterofmass: MIDERRFunction "miderr" is the secondary error function and derivatives for a distance geometry embedding; itincludes components from the distance bounds, local geometry, chirality and torsional restrainterrors MINIMIZ1Function "minimiz1" is a service routine that computes the energy and gradient for a low storage BFGSoptimizationinCartesiancoordinatespace MINIMIZEProgram "minimize"performsenergyminimization inCartesiancoordinatespaceusinga lowstorageBFGSnonlinearoptimization MINIROTProgram "minirot" performs an energy minimization in torsional angle space using a low storage BFGSnonlinearoptimization MINIROT1Function "minirot1" is a service routine that computes the energy and gradient for a low storage BFGSnonlinearoptimizationintorsionalanglespace MINPATHSubroutine "minpath"isaroutineforfindingthetrianglesmoothedupperandlowerboundsofeachatomtoaspecifiedrootatomusingasparsevariantoftheBellman-Fordshortestpathalgorithm MINRIGIDProgram "minrigid" performsan energyminimization of rigid body atomgroups using a low storageBFGSnonlinearoptimization


MINRIGID1Function "minrigid1" is a service routine that computes the energy and gradient for a low storage BFGSnonlinearoptimizationofrigidbodies MMIDSubroutine "mmid" implementsamodifiedmidpointmethod toadvance the integrationofa setof firstorderdifferentialequations MODECARTSubroutine MODEROTSubroutine MODESRCHSubroutine MODETORSSubroutine MODULISubroutine "moduli"setsthemodulioftheinversediscreteFouriertransformoftheB-splines;bsmod[1-3]holdthesevalues,nfft[1-3]arethegriddimensions,bsorderistheorderofB-splineapproximation MOLECULESubroutine "molecule"countsthemolecules,assignseachatomtoitsmoleculeandcomputesthemassofeachmolecule MOLUINDSubroutine "moluind"computesthemolecularinduceddipolecomponentsinthepresenceofanexternalelectricfield MOMENTSSubroutine "moments"computesthetotalelectriccharge,dipoleandquadrupolemomentsfortheentiresystemasasumoverthepartialcharges,bonddipolesandatomicmultipolemoments MONTEProgram "monte"performsaMonteCarlo/MCMconformationalsearchusingeitherCartesiansingleatomortorsionalmovesets MUTATESubroutine "mutate" constructs the hybrid hamiltonian for a specified initial state, final state and mutationparameter"lambda"


NEEDUPDATESubroutine NEIGHBORSubroutine "neighbor"findsalloftheneighborsofeachatom NEWATMSubroutine "newatm"createsanddefinesanatomneededfortheCartesiancoordinatesfile,butwhichmaynotpresentintheoriginalProteinDataBankfile NEWTONProgram "newton"performsanenergyminimizationinCartesiancoordinatespaceusingatruncatedNewtonmethod NEWTON1Function "newton1" is a service routine that computes the energy and gradient for truncated NewtonoptimizationinCartesiancoordinatespace NEWTON2Subroutine "newton2" is a service routine that computes the sparse matrix Hessian elements for truncatedNewtonoptimizationinCartesiancoordinatespace NEWTROTProgram "newtrot" performs an energy minimization in torsional angle space using a truncated Newtonconjugategradientmethod NEWTROT1Function "newtrot1" is a service routine that computes the energy and gradient for truncated Newtonconjugategradientoptimizationintorsionalanglespace NEWTROT2Subroutine "newtrot2" is a service routine that computes the sparse matrix Hessian elements for truncatedNewtonoptimizationintorsionalanglespace NEXTARGSubroutine "nextarg"findsthenextunusedcommandlineargumentandreturnsitintheinputcharacterstring NEXTTEXTFunction "nexttext"findsandreturnsthelocationofthefirstnon-blankcharacterwithinaninputtextstring;zeroisreturnedifnosuchcharacterisfound


NORMALFunction "normal"generatesarandomnumberfromanormalGaussiandistributionwithameanofzeroandavarianceofone NUCBASESubroutine "nucbase"buildsthesidechainforasinglenucleotidebaseintermsofinternalcoordinates NUCCHAINSubroutine "nucchain" builds up the internal coordinates for a nucleic acid sequence from the sugar type,backboneandglycosidictorsionalvalues NUCLEICProgram "nucleic" builds the internal and Cartesian coordinates of a polynucleotide from nucleic acidsequenceandtorsionalanglevaluesforthenucleicacidbackboneandsidechains NUMBERFunction "number"convertsatextnumeralintoanintegervalue;theinputstringmustcontainonlynumericcharacters NUMERALSubroutine "numeral" converts an input integer number into the corresponding right- or left-justified textnumeral NUMGRADSubroutine "numgrad" computes the gradient of the objective function "fvalue" with respect to Cartesiancoordinatesoftheatomsviaatwo-sidednumericaldifferentiation OCVMSubroutine "ocvm" is an optimally conditioned variable metric nonlinear optimization routine without linesearches OLDATMSubroutine "oldatm"gettheCartesiancoordinatesforanatomfromtheProteinDataBankfile,thenassignstheatomtypeandatomicconnectivities OPENENDSubroutine "openend"opensafileonaFortranunitsuchthatthepositionissettothebottomforappendingtotheendofthefile


OPTIMIZ1Function "optimiz1" is a service routine that computes the energy and gradient for optimally conditionedvariablemetricoptimizationinCartesiancoordinatespace OPTIMIZEProgram "optimize" performs energy minimization in Cartesian coordinate space using an optimallyconditionedvariablemetricmethod OPTIROTProgram "optirot"performsanenergyminimizationintorsionalanglespaceusinganoptimallyconditionedvariablemetricmethod OPTIROT1Function "optirot1" is a service routine that computes the energy and gradient for optimally conditionedvariablemetricoptimizationintorsionalanglespace OPTRIGIDProgram "optrigid" performs an energy minimization of rigid body atom groups using an optimallyconditionedvariablemetricmethod OPTRIGID1Function "optrigid1" is a service routine that computes the energy and gradient for optimally conditionedvariablemetricoptimizationofrigidbodies OPTSAVESubroutine "optsave" is used by the optimizers to write imtermediate coordinates and other relevantinformation;alsochecksforuserrequestedterminationofanoptimization ORBITALSubroutine "orbital" finds and organizes lists of atoms in a pisystem, bonds connecting pisystem atoms andtorsionswhosetwocentralatomsarebothpisystematoms ORIENTSubroutine "orient" computes a set of reference Cartesian coordinates in standard orientation for each rigidbodyatomgroup ORTHOGSubroutine "orthog"performsanorthogonalizationofaninputmatrixviathemodifiedGram-Schmidtalgorithm


OVERLAPSubroutine "overlap"computestheoverlapfortwoparallelp-orbitalsgiventheatomicnumbersanddistanceofseparation PARAMYZESubroutine "paramyze"printstheforcefieldparametersusedinthecomputationofeachofthepotentialenergyterms PASSBSubroutine PASSB2Subroutine PASSB3Subroutine PASSB4Subroutine PASSB5Subroutine PASSFSubroutine PASSF2Subroutine PASSF3Subroutine PASSF4Subroutine PASSF5Subroutine PATHProgram "path"locatesaseriesofstructuresequallyspacedalongaconformationalpathwayconnectingtheinputreactantandproductstructures;aseriesofconstrainedoptimizationsorthogonaltothepathisdoneviaLagrangianmultipliers PATH1Function PATHPNTSubroutine "pathpnt"findsastructureonthesynchronoustransitpathwiththespecifiedpathvalue"t" PATHSCANSubroutine "pathscan"makesascanofasynchronoustransitpathwaybycomputingstructuresandenergiesforspecificpathvalues PATHVALSubroutine


"pathval"computesthesynchronoustransitpathvalueforthespecifiedstructure PDBATMSubroutine "pdbatm"addsanatomtotheProteinDataBankfile PDBXYZProgram "pdbxyz" takes as input a ProteinDataBank file and then converts to andwrites out a Cartesiancoordinatesfileand,forbiopolymers,asequencefile PIALTERSubroutine "pialter" first modifies bond lengths and force constants according to the standard bond slopeparametersandthebondordervaluesstoredin"pnpl";alsoalterssome2-foldtorsionalparametersbasedonthebond-order*betamatrix PIMOVESubroutine "pimove"rotatesthevectorbetweenatoms"list(1)"and"list(2)"sothatatom1isattheoriginandatom2 along the x-axis; the atomsdefining the respective planes are alsomoved and their bondlengthsnormalized PIPLANESubroutine "piplane"selectsthethreeatomswhichspecifytheplaneperpendiculartoeachp-orbital;thecurrentversionwillfailincertainsituations,includingketenes,allenes,andisolatedoradjacenttriplebonds PISCFSubroutine "piscf"performsanscfmolecularorbitalcalculationforthepisystemusingamodifiedPariser-Parr-Poplemethod PITILTSubroutine "pitilt"calculatesforeachpibondtheratiooftheactualp-orbitaloverlapintegraltotheidealoverlapifthesameorbitalswereperfectlyparallel PLACESubroutine "place"findstheprobesitesbyputtingtheprobespheretangenttoeachtripleofneighboringatoms POLARGRPSubroutine "polargrp"generatesmembersofthepolarizationgroupofeachatomandseparatelistsofthe1-2,1-3and1-4groupconnectivities POLARIZEProgram


"polarize" computes the molecular polarizability by applying an external field along each axisfollowedbydiagonalizationoftheresultingpolarizabilitytensor POLYMERSubroutine "polymer"testsforthepresenceofaninfinitepolymerextendingacrossperiodicboundaries POLYPSubroutine "polyp"isapolynomialproductroutinethatmultipliestwoalgebraicforms POTNRGFunction POTOFFSubroutine "potoff"clearstheforcefielddefinitionbyturningofftheuseofeachofthepotentialenergyfunctions POWERSubroutine "power" uses the power method with deflation to compute the few largest eigenvalues andeigenvectorsofasymmetricmatrix PRECISEFunction "precise"findsamachineprecisionvalueasselectedbytheinputargument:(1)thesmallestpositivefloatingpointvalue,(2)thesmallestrelativefloatingpointspacing,(3)thelargestrelativefloatingpointspacing PRECONDSubroutine "precond" solves a simplified version of the Newton equations Ms = r, and uses the result topreconditionlinearconjugategradientiterationsonthefullNewtonequationsin"tnsolve" PRESSURESubroutine "pressure"uses the internalvirial to find thepressure inaperiodicboxandmaintainsaconstantdesiredpressurebyscalingthecoordinatesviacouplingtoanexternalconstantpressurebath PRMKEYSubroutine "field"parsesatextstringtoextractkeywordsrelatedtoforcefieldpotentialenergyfunctionalformsandconstants PROCHAINSubroutine "prochain"buildsup the internal coordinates foranaminoacidsequencefromthephi,psi,omegaandchivalues


PROJCTSubroutine PROMOSubroutine "promo"writesashortmessagecontaininginformationabouttheTINKERversionnumberandthecopyrightnotice PROPERTYFunction "property"takestwoinputsnapshotframesandcomputesthevalueofthepropertyforwhichthecorrelationfunctionisbeingaccumulated PROPYZESubroutine "propyze" finds and prints the total charge, dipole moment components, radius of gyration andmomentsofinertia PROSIDESubroutine "proside"buildsthesidechainforasingleaminoacidresidueintermsofinternalcoordinates PROTEINProgram "protein"buildstheinternalandCartesiancoordinatesofapolypeptidefromaminoacidsequenceandtorsionalanglevaluesforthepeptidebackboneandsidechains PRTARCSubroutine "prtarc"writes out a set of Cartesian coordinates for all active atoms in the TINKERXYZ archiveformat PRTCARSubroutine "prtcar"writesoutasetofCartesiancoordinatesforallactiveatomsintheAccelerysInsightII .carformat PRTDYNSubroutine "prtdyn"writesouttheinformationneededtorestartamoleculardynamicstrajectorytoanexternaldiskfile PRTERRSubroutine "prterr"writesoutasetofcoordinatestoadiskfilepriortoabortingonaseriouserror PRTINTSubroutine "prtint"writesoutasetofZ-matrixinternalcoordinatestoanexternaldiskfile


PRTMOL2Program "prtmol2"writesoutasetofcoordinatesinSybylMOL2formattoanexternaldiskfile PRTPDBSubroutine "prtpdb"writesoutasetofProteinDataBankcoordinatestoanexternaldiskfile PRTPRMSubroutine "prtprm"writesoutaformattedlistingofthedefaultsetofpotentialenergyparametersforaforcefield PRTSEQSubroutine "prtseq"writes out a biopolymer sequence to an external disk filewith 15 residues per line anddistinctchainsseparatedbyblanklines PRTXMOLSubroutine "prtxmol" writes out a set of Cartesian coordinates for all active atoms in a simple, generic XYZformatoriginallyusedbytheXMOLprogram PRTXYZSubroutine "prtxyz"writesoutasetofCartesiancoordinatestoanexternaldiskfile PSSProgram "pss" implements thepotential smoothingplussearchmethod forglobaloptimization inCartesiancoordinatespacewithlocalsearchesperformedinCartesianortorsionalspace PSS1Function "pss1"isaserviceroutinethatcomputestheenergyandgradientduringPSSglobaloptimizationinCartesiancoordinatespace PSS2Subroutine "pss2" is a service routine that computes the sparse matrix Hessian elements during PSS globaloptimizationinCartesiancoordinatespace PSSRGD1Function "pssrgd1"isaserviceroutinethatcomputestheenergyandgradientduringPSSglobaloptimizationoverrigidbodies PSSRIGIDProgram


"pssrigid"implementsthepotentialsmoothingplussearchmethodforglobaloptimizationforasetofrigidbodies PSSROTProgram "pssrot"implementsthepotentialsmoothingplussearchmethodforglobaloptimizationintorsionalspace PSSROT1Function "pssrot1"isaserviceroutinethatcomputestheenergyandgradientduringPSSglobaloptimizationintorsionalspace PSSWRITESubroutine PTINCYFunction PZEXTRSubroutine "pzextr" is a polynomial extrapolation routine used during Bulirsch-Stoer integration of ordinarydifferentialequations QRFACTSubroutine "qrfact" performsHouseholder transformationswith column pivoting (optional) to compute a QRfactorizationofthembynmatrixa;theroutinedeterminesanorthogonalmatrixq,apermutationmatrixp,andanuppertrapezoidalmatrixrwithdiagonalelementsofnonincreasingmagnitude,suchthata*p=q*r;theHouseholdertransformationforcolumnk,k=1,2,...,min(m,n),isoftheform QRSOLVESubroutine "qrsolve" solves a*x=b and d*x=0 in the least squares sense; normally used in combinationwithroutine"qrfact"tosolveleastsquaresproblems QUATFITSubroutine "quatfit" uses a quaternion-based method to achieve the best fit superposition of two sets ofcoordinates RADIALProgram "radial"findstheradialdistributionfunctionforaspecifiedpairofatomtypesviaanalysisofasetofcoordinateframes RANDOMFunction "random" generates a random number on [0,1] via a long period generator due to L'EcuyerwithBays-Durhamshuffle RANVECSubroutine


"ranvec" generates a unit vector in 3-dimensional space with uniformly distributed randomorientation RATTLESubroutine "rattle"implementsthefirstportionoftherattlealgorithmbycorrectingatomicpositionsandhalf-stepvelocitiestomaintaininteratomicdistanceandabsolutespatialconstraints RATTLE2Subroutine "rattle2"implementsthesecondportionoftherattlealgorithmbycorrectingthefull-stepvelocitiesinordertomaintaininteratomicdistanceconstraints READBLKSubroutine "readblk"readsinasetofsnapshotframesandtransfersthevaluestointernalarraysforuseinthecomputationoftimecorrelationfunctions READDYNSubroutine "readdyn"get thepositions,velocitiesandaccelerations foramoleculardynamics restart fromanexternaldiskfile READINTSubroutine "readint"getsasetofZ-matrixinternalcoordinatesfromanexternalfile READMOL2Subroutine "readmol2"getsasetofSybylMOL2coordinatesfromanexternaldiskfile READPDBSubroutine "readpdb"getsasetofProteinDataBankcoordinatesfromanexternaldiskfile READPRMSubroutine "readprm"processes the potential energy parameter file in order to define the default force fieldparameters READSEQSubroutine "readseq"getsabiopolymersequencecontainingoneormoreseparatechainsfromanexternalfile;alllinescontainingsequencemustbeginwiththestartingsequencenumber,theactualsequenceisreadfromsubsequentnonblankcharacters READXYZSubroutine


"readxyz"getsasetofCartesiancoordinatesfromanexternaldiskfile REFINESubroutine "refine" performs minimization of the atomic coordinates of an initial crude embedded distancegeometrystructureversusthebound,chirality,planarityandtorsionalerrorfunctions RELEASEMONITORSubroutine REPLICASubroutine "replica"decidesbetweenimagesandreplicatesforgenerationofperiodicboundaryconditions,andsetsthecellreplicatelistifthereplicatesmethodistobeused RFINDEXSubroutine "rfindex"findsindicesforeachmultipolesiteforuseincomputingreactionfieldenergetics RGDSRCHSubroutine RGDSTEPSubroutine "rgdstep"performsasinglemoleculardynamicstimestepforarigidbodycalculation RIBOSOMESubroutine "ribosome"translatesapolypeptidestructureinProteinDataBankformattoaCartesiancoordinatefileandsequencefile RIGIDXYZSubroutine "rigidxyz" computes Cartesian coordinates for a rigid body group via rotation and translation ofreferencecoordinates RINGSSubroutine "rings"searchesthestructureforsmallringsandstorestheirconstituentatoms RMSERRORSubroutine "rmserror" computes the maximum absolute deviation and the rms deviation from the distancebounds,andthenumberandrmsvalueofthedistancerestraintviolations RMSFITFunction "rmsfit"computesthermsfitoftwocoordinatesets ROTANGFunction


ROTCHECKFunction "rotcheck"testsaspecifiedcandidaterotatablebondforthedisallowedcasewhereinactiveatomsarefoundonbothsidesofthecandidatebond ROTEULERSubroutine "roteuler"computesasetofEuleranglevaluesconsistentwithaninputrotationmatrix ROTLISTSubroutine "rotlist"generates theminimum listofall theatoms lying toonesideofapairofdirectlybondedatoms;optionallyfindstheminimallistbychoosingthesidewithfeweratoms ROTMATSubroutine "rotmat"findstherotationmatrixthatconvertsfromthelocalcoordinatesystemtotheglobalframeatamultipolesite ROTPOLESubroutine "rotpole"constructsthesetofatomicmultipolesintheglobalframebyapplyingthecorrectrotationmatrixforeachsite ROTRGDSubroutine "rotrgd"findstherotationmatrixforarigidbodyduetoasinglestepofdynamics ROTSITESubroutine "rotsite" computes the atomic multipoles at a specified site in the global coordinate frame byapplyingarotationmatrix SADDLEProgram "saddle"findsa transitionstatebetween twoconformationalminimausingacombinationof ideasfromthesynchronoustransit(Halgren-Lipscomb)andquadraticpath(Bell-Crighton)methods SADDLE1Function "saddle1"isaserviceroutinethatcomputestheenergyandgradientfortransitionstateoptimization SADDLESSubroutine "saddles"constructscircles,convexedgesandsaddlefaces SCANProgram


"scan"attempts to findall the localminimaonapotentialenergysurfaceviaaniterativeseriesoflocalsearches SCAN1Function "scan1"isaserviceroutinethatcomputestheenergyandgradientduringexplorationofapotentialenergysurfaceviaiterativelocalsearch SCAN2Subroutine "scan2"isaserviceroutinethatcomputesthesparsematrixHessianelementsduringexplorationofapotentialenergysurfaceviaiterativelocalsearch SDAREASubroutine "sdarea"optionallyscalestheatomicfrictioncoefficientofeachatombasedonitsaccessiblesurfacearea SDSTEPSubroutine "sdstep"performsasinglestochasticdynamicstimestepviaavelocityVerletintegrationalgorithm SDTERMSubroutine "sdterm" gets frictional and random force terms needed to update positions and velocities viastochasticdynamics SEARCHSubroutine "search"isaunidimensionallinesearchbaseduponparabolicextrapolationandcubicinterpolationusingbothfunctionandgradientvalues;ifforcedtosearchinanuphilldirection,returnisaftertheinitialstep SETACCELERATIONSubroutine SETATOMICSubroutine SETATOMTYPESSubroutine SETCHARGESubroutine SETCONNECTIVITYSubroutine SETCOORDINATESSubroutine SETENERGYSubroutine SETFILESubroutine


SETFORCEFIELDSubroutine SETGRADIENTSSubroutine SETIMESubroutine "setime"initializestheelapsedintervalCPUtimer SETINDUCEDSubroutine SETKEYWORDSubroutine SETMASSSubroutine SETNAMESubroutine SETSTEPSubroutine SETSTORYSubroutine SETTIMESubroutine SETUPDATEDSubroutine SETVELOCITYSubroutine SHAKEUPSubroutine "shakeup" initializesanyholonomicconstraints forusewith the rattlealgorithmduringmoleculardynamics SIGMOIDFunction "sigmoid"implementsanormalizedsigmoidalfunctionontheinterval[0,1];thecurvesconnect(0,0)to(1,1)andhaveacooperativitycontrolledbybeta,theyapproachastraightlineasbeta->0andgetmorenonlinearasbetaincreases SKTDYNSubroutine "sktdyn"sendsthecurrentdynamicsinfoviaasocket SKTINITSubroutine "sktinit" sets up socket communicationwith the graphical user interface bystarting a Java virtualmachine,initiatingaserver,andloadinganobjectwithsysteminformation SKTKILLSubroutine "sktkill"closestheserverandJavavirtualmachine


SKTOPTSubroutine "sktopt"sendsthecurrentoptimizationinfoviaasocket SLATERSubroutine "slater"isageneralroutineforcomputingtheoverlapintegralsbetweentwoSlater-typeorbitals SMOOTHSubroutine "smooth" sets the type of smoothingmethod and the extent of surface deformation for usewithpotentialenergysmoothing SNIFFERProgram "sniffer"performsaglobalenergyminimizationusingadiscreteversionofGriewank'sglobalsearchtrajectory SNIFFER1Function "sniffer1" is a service routine that computes the energy and gradient for the Sniffer globaloptimizationmethod SOAKSubroutine "soak"takesacurrentlydefinedsolutesystemandplacesitintoasolventbox,withremovalofanysolventmoleculesthatoverlapthesolute SORTSubroutine "sort"takesaninputlistofintegersandsortsitintoascendingorderusingtheHeapsortalgorithm SORT10Subroutine "sort10"takesaninputlistofcharacterstringsandsortsitintoalphabeticalorderusingtheHeapsortalgorithm,duplicatevaluesareremovedfromthefinalsortedlist SORT2Subroutine "sort2"takesaninputlistofrealsandsortsitintoascendingorderusingtheHeapsortalgorithm;italsoreturnsakeyintotheoriginalordering SORT3Subroutine "sort3"takesaninputlistofintegersandsortsitintoascendingorderusingtheHeapsortalgorithm;italsoreturnsakeyintotheoriginalordering SORT4Subroutine


"sort4"takesaninput listofintegersandsorts it intoascendingabsolutevalueusingtheHeapsortalgorithm SORT5Subroutine "sort5"takesaninputlistofintegersandsortsitintoascendingorderbasedoneachvaluemodulo"m" SORT6Subroutine "sort6"takesaninputlistofcharacterstringsandsortsitintoalphabeticalorderusingtheHeapsortalgorithm SORT7Subroutine "sort7"takesaninputlistofcharacterstringsandsortsitintoalphabeticalorderusingtheHeapsortalgorithm;italsoreturnsakeyintotheoriginalordering SORT8Subroutine "sort8"takesaninputlistofintegersandsortsitintoascendingorderusingtheHeapsortalgorithm,duplicatevaluesareremovedfromthefinalsortedlist SORT9Subroutine "sort9" takesan input listof realsandsorts it intoascendingorderusing theHeapsortalgorithm,duplicatevaluesareremovedfromthefinalsortedlist SPACEFILLProgram "spacefill" computes the surface area and volume of a structure; the van der Waals, accessible-excluded,andcontact-reentrantdefinitionsareavailable SPECTRUMProgram "spectrum"computesapowerspectrumoverawavelengthrangefromthevelocityautocorrelationasafunctionoftime SQUARESubroutine "square" is a nonlinear least squares routine derived from the IMSL routine BCLSF and More'sMinpackroutineLMDER;theJacobianisestimatedbyfinitedifferencesandboundscanbespecifiedforthevariablestoberefined SUFFIXSubroutine "suffix"checksafilenameforthepresenceofanextension,andappendsanextensionifnoneisfound SUPERPOSEProgram


"superpose"takespairsofstructuresandsuperimposesthemintheoptimal leastsquaressense;itwillattempttomatchallatompairsoronlythosespecifiedbytheuser SURFACESubroutine "surface"performsananalyticalcomputationoftheweightedsolventaccessiblesurfaceareaofeachatomandthefirstderivativesoftheareawithrespecttoCartesiancoordinates SURFATOMSubroutine "surfatom"performsananalyticalcomputationofthesurfaceareaofaspecifiedatom;asimplifiedversionof"surface" SWITCHSubroutine "switch"setsthecoeffcientsusedbythefifthandseventhorderpolynomialswitchingfunctionsforsphericalcutoffs SYBYLXYZProgram "sybylxyz" takesas inputaSybylMOL2coordinatesfile, converts toand thenwritesoutCartesiancoordinates SYMMETRYSubroutine "symmetry" applies symmetry operators to the fractional coordinates of the asymmetric unit inordertogeneratethesymmetryrelatedatomsofthefullunitcell TANGENTSubroutine "tangent"findstheprojectedgradientonthesynchronoustransitpathforapointalongthetransitpathway TEMPERSubroutine "temper"appliesavelocitycorrectionatthehalftimestepasneededfortheNose-Hooverextendedsystemthermostat TEMPER2Subroutine "temper2"computestheinstantaneoustemperatureandappliesathermostatviaBerendsenvelocityscaling,Andersenstochasticcollisions,LangevinpistonorNose-Hooverextendedsystems TESTGRADProgram "testgrad" computes and compares the analytical and numerical gradient vectors of the potentialenergyfunctionwithrespecttoCartesiancoordinates TESTHESSProgram


"testhess" computes and compares the analytical andnumericalHessianmatrices of the potentialenergyfunctionwithrespecttoCartesiancoordinates TESTLIGHTProgram "testlight" performs a set of timing tests to compare the evaluation of potential energy andenergy/gradientusingthemethodoflightswithadoubleloopoverallatompairs TESTROTProgram "testrot" computes and compares the analytical and numerical gradient vectors of the potentialenergyfunctionwithrespecttorotatabletorsionalangles TIMERProgram "timer"measurestheCPUtimerequiredforfilereadingandparameterassignment,potentialenergycomputation,energyandgradientcomputation,andHessianmatrixevaluation TIMEROTProgram "timerot" measures the CPU time required for file reading and parameter assignment, potentialenergy computation, energy and gradient over torsions, and torsional angle Hessian matrixevaluation TNCGSubroutine "tncg" implements a truncated Newton optimization algorithm in which a preconditioned linearconjugate gradient method is used to approximately solve Newton's equations; special featuresinclude use ofan explicit sparseHessian or finite-difference gradient-Hessianproductswithin thePCG iteration; theexactNewtonsearchdirectionscanbeusedoptionally;bydefault thealgorithmchecks for negative curvature to prevent convergence to a stationary point having negativeeigenvalues;ifasaddlepointisdesiredthistestcanberemovedbydisabling"negtest" TNSOLVESubroutine "tnsolve"usesalinearconjugategradientmethodtofindanapproximatesolutiontothesetoflinearequationsrepresentedinmatrixformbyHp=-g(Newton'sequations) TORPHASESubroutine "torphase" sets the n-fold amplitude and phase values for each torsion via sorting of the inputparameters TORQUESubroutine "torque"takesthetorquevaluesonsitesdefinedbylocalcoordinateframesanddistributesthmetoconverttoforcesontheoriginalsitesandsitesspecifyingthelocalframes TORQUE1Subroutine


"torque1"takesthetorquevalueonasitedefinedbyalocalcoordinateframeanddistributesittoconverttoforcesontheoriginalsiteandsitesspecifyingthelocalframe TORSERFunction "torser" computes the torsional error function and its first derivativeswith respect to the atomicCartesiancoordinatesbasedon thedeviationofspecified torsionalangles fromdesiredvalues, thecontainedbondanglesarealsorestrainedtoavoidanumericalinstability TORSIONSSubroutine "torsions"findsthetotalnumberofdihedralanglesandthenumbersofthefouratomsdefiningeachdihedralangle TORUSSubroutine "torus"setsalistofallofthetemporarytoruspositionsbytestingforatorusbetweeneachatomanditsneighbors TOTERRFunction "toterr" is the error function and derivatives for a distance geometry embedding; it includescomponentsfromthedistancebounds,hardspherecontacts,localgeometry,chiralityandtorsionalrestrainterrors TRANSITFunction "transit"evaluatesthesynchronoustransitfunctionandgradient;linearandquadratictransitpathsareavailable TRIANGLESubroutine "triangle" smooths the upper and lower distance bounds via the triangle inequality using a full-matrix variant of the Floyd-Warshall shortest path algorithm; this routine is usuallymuch slowerthanthesparsematrixshortestpathmethodsin"geodesic"and"trifix",andshouldbeusedonlyforcomparisonwithanswersgeneratedbythoseroutines TRIFIXSubroutine "trifix" rebuilds both the upper and lower distance boundmatrices following tightening of one orboth of the bounds between a specified pair of atoms, "p" and "q", using a modification ofMurchland'sshortestpathupdatealgorithm TRIMTEXTFunction "trimtext"findsandreturnsthelocationofthelastnon-blankcharacterbeforethefirstnullcharacterinaninputtextstring;thefunctionreturnszeroifnosuchcharacterisfound TRIPLEFunction


"triple" finds the tripleproductof threevectors;usedasa service routineby theConnolly surfaceareaandvolumecomputation TRUSTSubroutine "trust"updatesthemodeltrustregionforanonlinearleastsquarescalculation;thisversionisbasedontheideasfoundinNL2SOLandinDennisandSchnabel'sbook UDIRECT1Subroutine "udirect1"computesthereciprocalspacecontributionofthepermanentatomicmultipolemomentsto theelectrostatic field for use in finding the direct induceddipolemoments via a regular Ewaldsummation UDIRECT2Subroutine "udirect2"computestherealspacecontributionofthepermanentatomicmultipolemomentstotheelectrostatic field for use in finding the direct induced dipole moments via a regular Ewaldsummation UFIELDSubroutine "ufield" finds the field at eachpolarizable site due to the induceddipoles at the other sites usingThole'smethodtodampthefieldatcloserange UMUTUAL1Subroutine "umutual1"computesthereciprocalspacecontributionoftheinducedatomicdipolemomentstotheelectrostatic field for use in iterative calculation of induced dipole moments via a regular Ewaldsummation UMUTUAL2Subroutine "umutual2" computes the real space contribution of the induced atomic dipole moments to theelectrostatic field for use in iterative calculation of induced dipole moments via a regular Ewaldsummation UNITCELLSubroutine "unitcell"getstheperiodicboundaryboxsizeandrelatedvaluesfromanexternalkeywordfile UPCASESubroutine "upcase"convertsatextstringtoalluppercaseletters VAMSubroutine "vam" takes the analytical molecular surface defined as a collection of spherical and toroidalpolygonsandusesittocomputethevolumeandsurfacearea


VCROSSSubroutine "vcross"findsthecrossproductoftwovectors VDWERRFunction "vdwerr"isthehardspherevanderWaalsbounderrorfunctionandderivativesthatpenalizesclosenonbondedcontacts,pairwiseneighborsaregeneratedviathemethodoflights VECANGFunction "vecang"findstheanglebetweentwovectorshandedwithrespecttoacoordinateaxis;returnsanangleintherange[0,2*pi] VERLETSubroutine "verlet"performsa singlemoleculardynamics timestepbymeansof thevelocityVerletmultisteprecursionformula VERSIONSubroutine "version"checksthenameofafileabouttobeopened; if if"old"statusispassed,thenameofthehighest current version is returned; if "new" status is passed the filename of the next availableunusedversionisgenerated VIBRATEProgram "vibrate"performsavibrationalnormalmodeanalysis;theHessianmatrixofsecondderivativesisdetermined and then diagonalized both directly and aftermassweighting; output consists of theeigenvaluesoftheforceconstantmatrixaswellasthevibrationalfrequenciesanddisplacements VIBRIGIDProgram "vibrigid"computestheeigenvaluesandeigenvectorsoftheHessianmatrixoverrigidbodydegreesoffreedom VIBROTProgram "vibrot"computestheeigenvaluesandeigenvectorsofthetorsionalHessianmatrix VNORMSubroutine "vnorm"normalizesavectortounit length;usedasaserviceroutinebytheConnollysurfaceareaandvolumecomputation VOLUMESubroutine "volume" calculates the excluded volume via the Connolly analytical volume and surface areaalgorithm


VOLUME1Subroutine "volume1" calculates first derivatives of the total excluded volume with respect to the Cartesiancoordinatesofeachatom VOLUME2Subroutine "volume2"calculatessecondderivativesofthetotalexcludedvolumewithrespecttotheCartesiancoordinatesoftheatoms WATSONSubroutine "watson"usesarigidbodyoptimizationtoapproximatelyalignthepairedstrandsofanucleicaciddoublehelix WATSON1Function "watson1" is a service routine that computes the energy and gradient for optimally conditionedvariablemetricoptimizationofrigidbodies XTALERRSubroutine "xtalerr" computes an error function value derived from derivatives with respect to latticeparameters,latticeenergyandmonomerdipolemoments XTALFITProgram "xtalfit"computesanoptimizedsetofpotentialenergyparametersforuserspecifiedvanderWaalsand electrostatic interactions by fitting to crystal structure, lattice energy and monomer dipolemomentdata XTALLAT1Function "xtalmol1"isaserviceroutinethatcomputestheenergyandnumericalgradientwithrespecttothesixlatticelengthsandanglesforacrystalenergyminimization XTALMINProgram "xtalmin" performs a full crystal energy minimization by alternating cycles of truncated Newtonoptimization over atomic coordinates with variable metric optimization over the six latticedimensionsandangles XTALMOL1Function "xtalmol1" is a service routine that computes the energy and gradientwith respect to the atomicCartesiancoordinatesforacrystalenergyminimization XTALMOL2Subroutine


"xtalmol2"isaserviceroutinethatcomputesthesparsematrixHessianelementswithrespecttotheatomicCartesiancoordinatesforacrystalenergyminimization XTALMOVESubroutine "xtalmove" converts fractional to Cartesian coordinates for rigidmolecules during fitting of forcefieldparameterstocrystalstructuredata XTALPRMSubroutine "xtalprm" stores or retrieves a crystal structure; used to make a previously stored structure thecurrentlyactivestructure,ortostoreastructureforlateruse;onlyprovidesfortheintermolecularenergyterms XTALWRTSubroutine "xtalwrt"isautilitythatprintsintermediateresultsduringfittingofforcefieldparameterstocrystaldata XYZATMSubroutine "xyzatm"computestheCartesiancoordinatesofasingleatomfromitsdefininginternalcoordinatevalues XYZEDITProgram "xyzedit"providesformodificationandmanipulationofthecontentsofaCartesiancoordinatesfile XYZINTProgram "xyzint" takes as input a Cartesian coordinates file, then converts to and writes out an internalcoordinatesfile XYZPDBProgram "xyzpdb"takesasinputaCartesiancoordinatesfile,thenconvertstoandwritesoutaProteinDataBankfile XYZRIGIDSubroutine "xyzrigid"computesthecenterofmassandEuleranglerigidbodycoordinatesforeachatomgroupinthesystem XYZSYBYLProgram "xyzsybyl"takesasinputaCartesiancoordinatesfile,convertstoandthenwritesoutaSybylMOL2file ZATOMSubroutine


"zatom"addsanatomtotheendofthecurrentZ-matrixandthenincrementstheatomcounter;atomtype,definingatomsandinternalcoordinatesarepassedasarguments ZHELPSubroutine "zhelp"printsthegeneralinformationandinstructionsfortheZ-matrixeditingprogram ZVALUESubroutine "zvalue" gets user supplied values for selected coordinates as needed by the internal coordinateeditingprogram


10. DescriptionsofGlobalVariables The Fortran common blocks found in the TINKER package are listed below along with a briefdescriptionofthecontentsofeachvariableineachcommonblock.Eachindividualcommonblockispresentasaseparate".i"fileinthe/sourcesubdirectory.Asourcecodelistingcontainingeachofthesourcecodemodulesandeachofthecommonblockscanbeproducedbyrunningthe"listing.make"scriptfoundinthedistribution. ACTION totalnumberofeachenergytermcomputed neb numberofbondstretchenergytermscomputed nea numberofanglebendenergytermscomputed neba numberofstretch-bendenergytermscomputed neub numberofUrey-Bradleyenergytermscomputed neaa numberofangle-angleenergytermscomputed neopb numberofout-of-planebendenergytermscomputed neopd numberofout-of-planedistanceenergytermscomputed neid numberofimproperdihedralenergytermscomputed neit numberofimpropertorsionenergytermscomputed net numberoftorsionalenergytermscomputed nept numberofpi-orbitaltorsionenergytermscomputed nebt numberofstretch-torsionenergytermscomputed nett numberoftorsion-torsionenergytermscomputed nev numberofvanderWaalsenergytermscomputed nec numberofcharge-chargeenergytermscomputed necd numberofcharge-dipoleenergytermscomputed ned numberofdipole-dipoleenergytermscomputed nem numberofmultipoleenergytermscomputed nep numberofpolarizationenergytermscomputed new numberofEwaldsummationenergytermscomputed ner numberofreactionfieldenergytermscomputed nes numberofsolvationenergytermscomputed nelf numberofmetalligandfieldenergytermscomputed neg numberofgeometricrestraintenergytermscomputed nex numberofextraenergytermscomputed ALIGN informationforsuperpositionofstructures wfit weightsassignedtoatompairsduringsuperposition nfit numberofatomstouseinsuperimposingtwostructures ifit atomnumbersofpairsofatomstobesuperimposed ANALYZ energycomponentspartitionedoveratoms aesum totalpotentialenergypartitionedoveratoms aeb bondstretchenergypartitionedoveratoms aea anglebendenergypartitionedoveratoms aeba stretch-bendenergypartitionedoveratoms aeub Urey-Bradleyenergypartitionedoveratoms aeaa angle-angleenergypartitionedoveratoms aeopb out-of-planebendenergypartitionedoveratoms


aeopd out-of-planedistanceenergypartitionedoveratoms aeid improperdihedralenergypartitionedoveratoms aeit impropertorsionenergypartitionedoveratoms aet torsionalenergypartitionedoveratoms aept pi-orbitaltorsionenergypartitionedoveratoms aebt stretch-torsionenergypartitionedoveratoms aett torsion-torsionenergypartitionedoveratoms aev vanderWaalsenergypartitionedoveratoms aec charge-chargeenergypartitionedoveratoms aecd charge-dipoleenergypartitionedoveratoms aed dipole-dipoleenergypartitionedoveratoms aem multipoleenergypartitionedoveratoms aep polarizationenergypartitionedoveratoms aer reactionfieldenergypartitionedoveratoms aes solvationenergypartitionedoveratoms aelf metalligandfieldenergypartitionedoveratoms aeg geometricrestraintenergypartitionedoveratoms aex extraenergytermpartitionedoveratoms ANGANG angle-angletermsincurrentstructure kaa forceconstantforangle-anglecrossterms nangang totalnumberofangle-angleinteractions iaa anglenumbersusedineachangle-angleterm ANGLE bondangleswithinthecurrentstructure ak harmonicangleforceconstant(kcal/mole/rad**2) anat idealbondangleorphaseshiftangle(degrees) afld periodicityforFourierbondangleterm nangle totalnumberofbondanglesinthesystem iang numbersoftheatomsineachbondangle angtyp potentialenergyfunctiontypeforeachbondangle ANGPOT specificsofbondanglefunctionalforms cang cubiccoefficientinanglebendingpotential qang quarticcoefficientinanglebendingpotential pang quinticcoefficientinanglebendingpotential sang sexticcoefficientinanglebendingpotential angunit convertanglebendingenergytokcal/mole stbnunit convertstretch-bendenergytokcal/mole aaunit convertangle-angleenergytokcal/mole opbunit convertout-of-planebendenergytokcal/mole opdunit convertout-of-planedistanceenergytokcal/mole mm2stbn logicalflaggoverninguseofMM2-stylestretch-bend ARGUE commandlineargumentsatprogramstartup maxarg maximumnumberofcommandlinearguments narg numberofcommandlineargumentstotheprogram listarg flagtomarkavailablecommandlinearguments


arg stringscontainingthecommandlinearguments ATMLST localgeometrytermsinvolvingeachatom bndlist listofthebondnumbersinvolvingeachatom anglist listoftheanglenumberscenteredoneachatom ATMTYP atomicpropertiesforeachcurrentatom mass atomicweightforeachatominthesystem tag integeratomlabelsfrominputcoordinatesfile class atomclassnumberforeachatominthesystem atomic atomicnumberforeachatominthesystem valence valencenumberforeachatominthesystem name atomnameforeachatominthesystem story descriptivetypeforeachatominsystem ATOMS number,positionandtypeofcurrentatoms x currentx-coordinateforeachatominthesystem y currenty-coordinateforeachatominthesystem z currentz-coordinateforeachatominthesystem n totalnumberofatomsinthecurrentsystem type atomtypenumberforeachatominthesystem BATH temperatureandpressurecontrolparameters maxnose maximumlengthoftheNose-Hooverchain kelvin0 targetvalueforthesystemtemperature(K) kelvin variabletargettemperatureforthermostat(K) atmsph targetvalueforthesystempressure(atm) tautemp timeconstantforBerendsenthermostat(psec) taupres timeconstantforBerendsenbarostat(psec) compress isothermalcompressibilityofmedium(atm-1) collide collisionfrequencyforAndersenthermostat xnh positionofeachchainedNose-Hooverthermostat vnh velocityofeachchainedNose-Hooverthermostat qnh massforeachchainedNose-Hooverthermostat gnh couplingbetweenchainedNose-Hooverthermostats isothermal logicalflaggoverninguseoftemperaturecontrol isobaric logicalflaggoverninguseofpressurecontrol tempvary logicalflagtoenablevariabletargetthermostat thermostat choiceoftemperaturecontrolmethodtobeused barostat choiceofpressurecontrolmethodtobeused BITOR bitorsionswithinthecurrentstructure nbitor totalnumberofbitorsionsinthesystem ibitor numbersoftheatomsineachbitorsion BNDPOT specificsofbondstretchfunctionalforms


cbnd cubiccoefficientinbondstretchpotential qbnd quarticcoefficientinbondstretchpotential bndunit convertbondstretchenergytokcal/mole bndtyp typeofbondstretchpotentialenergyfunction BOND covalentbondsinthecurrentstructure bk bondstretchforceconstants(kcal/mole/Ang**2) bl idealbondlengthvaluesinAngstroms nbond totalnumberofbondstretchesinthesystem ibnd numbersoftheatomsineachbondstretch BORDER bondordersforaconjugatedpisystem pbpl pi-bondordersforbondsin"planar"pisystem pnpl pi-bondordersforbondsin"nonplanar"pisystem BOUND controlofperiodicboundaryconditions polycut cutoffdistanceforinfinitepolymernonbonds polycut2 squareofinfinitepolymernonbondcutoff use_bounds flagtouseperiodicboundaryconditions use_image flagtouseimagesforperiodicsystem use_replica flagtousereplicatesforperiodicsystem use_polymer flagtomarkpresenceofinfinitepolymer BOXES parametersforperiodicboundaryconditions xbox lengthinAngsofa-axisofperiodicbox ybox lengthinAngsofb-axisofperiodicbox zbox lengthinAngsofc-axisofperiodicbox alpha angleindegreesbetweenb-andc-axesofbox beta angleindegreesbetweena-andc-axesofbox gamma angleindegreesbetweena-andb-axesofbox xbox2 halfofthea-axislengthofperiodicbox ybox2 halfoftheb-axislengthofperiodicbox zbox2 halfofthec-axislengthofperiodicbox box34 three-fourthsaxislengthoftruncatedoctahedron recip reciprocallatticevectorsasmatrixcolumns volbox volumeinAng**3oftheperiodicbox beta_sin sineofthebetaperiodicboxangle beta_cos cosineofthebetaperiodicboxangle gamma_sin sineofthegammaperiodicboxangle gamma_cos cosineofthegammaperiodicboxangle beta_term termusedingeneratingtriclinicbox gamma_term termusedingeneratingtriclinicbox orthogonal flagtomarkperiodicboxasorthogonal monoclinic flagtomarkperiodicboxasmonoclinic triclinic flagtomarkperiodicboxastriclinic octahedron flagtomarkboxastruncatedoctahedron spacegrp spacegroupsymbolfortheunitcelltype


CELL periodicboundariesusingreplicatedcells xcell lengthofthea-axisofthecompletereplicatedcell ycell lengthoftheb-axisofthecompletereplicatedcell zcell lengthofthec-axisofthecompletereplicatedcell xcell2 halfthelengthofthea-axisofthereplicatedcell ycell2 halfthelengthoftheb-axisofthereplicatedcell zcell2 halfthelengthofthec-axisofthereplicatedcell ncell totalnumberofcellreplicatesforperiodicboundaries icell offsetalongaxesforeachreplicateperiodiccell CHARGE partialchargesforthecurrentstructure pchg magnitudeofthepartialcharges(e-) nion totalnumberofpartialchargesinsystem iion numberoftheatomsiteforeachpartialcharge jion neighborgenerationsiteforeachpartialcharge kion cutoffswitchingsiteforeachpartialcharge chglist partialchargesiteforeachatom(0=nocharge) CHGPOT specificsofcharge-chargefunctionalform dielec dielectricconstantforelectrostaticinteractions c2scale factorbywhich1-2chargeinteractionsarescaled c3scale factorbywhich1-3chargeinteractionsarescaled c4scale factorbywhich1-4chargeinteractionsarescaled c5scale factorbywhich1-5chargeinteractionsarescaled neutnbr logicalflaggoverninguseofneutralgroupneighbors neutcut logicalflaggoverninguseofneutralgroupcutoffs CHRONO timingstatisticsforthecurrentprogram cputim elapsedcputimeinsecondssincestartofprogram COUPLE near-neighboratomconnectivitylists maxn13 maximumnumberofatoms1-3connectedtoanatom maxn14 maximumnumberofatoms1-4connectedtoanatom maxn15 maximumnumberofatoms1-5connectedtoanatom n12 numberofatomsdirectlybondedtoeachatom i12 atomnumbersofatoms1-2connectedtoeachatom n13 numberofatomsina1-3relationtoeachatom i13 atomnumbersofatoms1-3connectedtoeachatom n14 numberofatomsina1-4relationtoeachatom i14 atomnumbersofatoms1-4connectedtoeachatom n15 numberofatomsina1-5relationtoeachatom i15 atomnumbersofatoms1-5connectedtoeachatom CUTOFF cutoffdistancesforenergyinteractions


vdwcut cutoffdistanceforvanderWaalsinteractions chgcut cutoffdistanceforcharge-chargeinteractions dplcut cutoffdistancefordipole-dipoleinteractions mpolecut cutoffdistanceforatomicmultipoleinteractions vdwtaper distanceatwhichvanderWaalsswitchingbegins chgtaper distanceatwhichcharge-chargeswitchingbegins dpltaper distanceatwhichdipole-dipoleswitchingbegins mpoletaper distanceatwhichatomicmultipoleswitchingbegins ewaldcut cutoffdistancefordirectspaceEwaldsummation use_ewald logicalflaggoverninguseofEwaldsummationterm use_lights logicalflagtousemethodoflightsneighbors DERIV Cartesiancoordinatederivativecomponents desum totalenergyCartesiancoordinatederivatives deb bondstretchCartesiancoordinatederivatives dea anglebendCartesiancoordinatederivatives deba stretch-bendCartesiancoordinatederivatives deub Urey-BradleyCartesiancoordinatederivatives deaa angle-angleCartesiancoordinatederivatives deopb out-of-planebendCartesiancoordinatederivatives deopd out-of-planedistanceCartesiancoordinatederivatives deid improperdihedralCartesiancoordinatederivatives deit impropertorsionCartesiancoordinatederivatives det torsionalCartesiancoordinatederivatives dept pi-orbitaltorsionCartesiancoordinatederivatives debt stretch-torsionCartesiancoordinatederivatives dett torsion-torsionCartesiancoordinatederivatives dev vanderWaalsCartesiancoordinatederivatives dec charge-chargeCartesiancoordinatederivatives decd charge-dipoleCartesiancoordinatederivatives ded dipole-dipoleCartesiancoordinatederivatives dem multipoleCartesiancoordinatederivatives dep polarizationCartesiancoordinatederivatives der reactionfieldCartesiancoordinatederivatives des solvationCartesiancoordinatederivatives delf metalligandfieldCartesiancoordinatederivatives deg geometricrestraintCartesiancoordinatederivatives dex extraenergytermCartesiancoordinatederivatives DIPOLE atom&bonddipolesforcurrentstructure bdpl magnitudeofeachofthedipoles(Debyes) sdpl positionofeachdipolebetweendefiningatoms ndipole totalnumberofdipolesinthesystem idpl numbersofatomsthatdefineeachdipole DISGEO distancegeometryboundsandparameters bnd distancegeometryupperandlowerboundsmatrix vdwrad hardsphereradiifordistancegeometryatoms vdwmax maximumvalueofhardspheresumforanatompair


compact indexoflocaldistancecompactiononembedding pathmax maximumvalueofupperboundaftersmoothing use_invert flagtouseenantiomerclosesttoinputstructure use_anneal flagtousesimulatedannealingrefinement DOMEGA derivativecomponentsovertorsions tesum totalenergyderivativesovertorsions teb bondstretchderivativesovertorsions tea anglebendderivativesovertorsions teba stretch-bendderivativesovertorsions teub Urey-Bradleyderivativesovertorsions teaa angle-anglederivativesovertorsions teopb out-of-planebendderivativesovertorsions teopd out-of-planedistancederivativesovertorsions teid improperdihedralderivativesovertorsions teit impropertorsionderivativesovertorsions tet torsionalderivativesovertorsions tept pi-orbitaltorsionderivativesovertorsions tebt stretch-torsionderivativesovertorsions tett torsion-torsionderivativesovertorsions tev vanderWaalsderivativesovertorsions tec charge-chargederivativesovertorsions tecd charge-dipolederivativesovertorsions ted dipole-dipolederivativesovertorsions tem atomicmultipolederivativesovertorsions tep polarizationderivativesovertorsions ter reactionfieldderivativesovertorsions tes solvationderivativesovertorsions telf metalligandfieldderivativesovertorsions teg geometricrestraintderivativesovertorsions tex extraenergytermderivativesovertorsions ENERGI individualpotentialenergycomponents esum totalpotentialenergyofthesystem eb bondstretchpotentialenergyofthesystem ea anglebendpotentialenergyofthesystem eba stretch-bendpotentialenergyofthesystem eub Urey-Bradleypotentialenergyofthesystem eaa angle-anglepotentialenergyofthesystem eopb out-of-planebendpotentialenergyofthesystem eopd out-of-planedistancepotentialenergyofthesystem eid improperdihedralpotentialenergyofthesystem eit impropertorsionpotentialenergyofthesystem et torsionalpotentialenergyofthesystem ept pi-orbitaltorsionpotentialenergyofthesystem ebt stretch-torsionpotentialenergyofthesystem ett torsion-torsionpotentialenergyofthesystem ev vanderWaalspotentialenergyofthesystem ec charge-chargepotentialenergyofthesystem ecd charge-dipolepotentialenergyofthesystem ed dipole-dipolepotentialenergyofthesystem


em atomicmultipolepotentialenergyofthesystem ep polarizationpotentialenergyofthesystem er reactionfieldpotentialenergyofthesystem es solvationpotentialenergyofthesystem elf metalligandfieldpotentialenergyofthesystem eg geometricrestraintpotentialenergyofthesystem ex extratermpotentialenergyofthesystem EWALD parametersforregularorPMEwaldsummation aewald Ewaldconvergencecoefficientvalue(Ang-1) frecip fractionalcutoffvalueforreciprocalsphere tinfoil flaggoverninguseoftinfoilboundaryconditions EWREG exponentialfactorsforregularEwaldsum maxvec maximumnumberofk-vectorsperreciprocalaxis ejc exponentalfactorsforcosinealongthej-axis ejs exponentalfactorsforsinealongthej-axis ekc exponentalfactorsforcosinealongthek-axis eks exponentalfactorsforsinealongthek-axis elc exponentalfactorsforcosinealongthel-axis els exponentalfactorsforsinealongthel-axis FACES variablesforConnollyareaandvolume maxnbr maximumnumberofneighboringatompairs maxtt maximumnumberoftemporarytori maxt maximumnumberoftotaltori maxp maximumnumberofprobepositions maxv maximumnumberofvertices maxen maximumnumberofconcaveedges maxfn maximumnumberofconcavefaces maxc maximumnumberofcircles maxep maximumnumberofconvexedges maxfs maximumnumberofsaddlefaces maxcy maximumnumberofcycles mxcyep maximumnumberofcycleconvexedges maxfp maximumnumberofconvexfaces mxfpcy maximumnumberofconvexfacecycles FIELDS molecularmechanicsforcefielddescription biotyp forcefieldatomtypeofeachbiopolymertype forcefield stringusedtodescribethecurrentforcefield FILES nameandnumberofcurrentstructurefiles nprior numberofpreviouslyexistingcyclefiles ldir lengthincharactersofthedirectoryname leng lengthincharactersofthebasefilename


filename basefilenameusedbydefaultforallfiles outfile outputfilenameusedforintermediateresults FRACS atomdistancestomolecularcenterofmass xfrac fractionalcoordinatealonga-axisofcenterofmass yfrac fractionalcoordinatealongb-axisofcenterofmass zfrac fractionalcoordinatealongc-axisofcenterofmass GROUP partitioningofsystemintoatomgroups grpmass totalmassofalltheatomsineachgroup wgrp weightforeachsetofgroup-groupinteractions ngrp totalnumberofatomgroupsinthesystem kgrp contiguouslistoftheatomsineachgroup igrp firstandlastatomofeachgroupinthelist grplist numberofthegrouptowhicheachatombelongs use_group flagtousepartitioningofsystemintogroups use_intra flagtoincludeonlyintragroupinteractions use_inter flagtoincludeonlyintergroupinteractions HESCUT cutoffvalueforHessianmatrixelements hesscut magnitudeofsmallestallowedHessianelement HESSN CartesianHessianelementsforasingleatom hessx Hessianelementsforx-componentofcurrentatom hessy Hessianelementsfory-componentofcurrentatom hessz Hessianelementsforz-componentofcurrentatom IMPROP improperdihedralsinthecurrentstructure kprop forceconstantvaluesforimproperdihedralangles vprop idealimproperdihedralanglevalueindegrees niprop totalnumberofimproperdihedralanglesinthesystem iiprop numbersoftheatomsineachimproperdihedralangle IMPTOR impropertorsionsinthecurrentstructure itors1 1-foldamplitudeandphaseforeachimpropertorsion itors2 2-foldamplitudeandphaseforeachimpropertorsion itors3 3-foldamplitudeandphaseforeachimpropertorsion nitors totalnumberofimpropertorsionalanglesinthesystem iitors numbersoftheatomsineachimpropertorsionalangle INFORM controlvaluesforI/Oandprogramflow digits decimalplacesoutputforenergyandcoordinates iprint stepsbetweenstatusprinting(0=noprinting) iwrite stepsbetweencoordinatedumps(0=nodumps)


isend stepsbetweensocketcommunication(0=nosockets) verbose logicalflagtoturnonextrainformation debug logicalflagtoturnonfulldebugprinting holdup logicalflagtowaitforcarriagereturnonexit abort logicalflagtostopexecutionatnextchance INTER sumofintermolecularenergycomponents einter totalintermolecularpotentialenergy IOUNIT Fortraninput/output(I/O)unitnumbers iout FortranI/Ounitformajoroutput(default=6) input FortranI/Ounitformajorinput(default=5) KANANG forcefieldparametersforangle-angleterms anan angle-anglecrosstermparametersforeachatomclass KANGS forcefieldparametersforbondanglebending maxna maximumnumberofharmonicanglebendparameterentries maxna5 maximumnumberof5-memberedringanglebendentries maxna4 maximumnumberof4-memberedringanglebendentries maxna3 maximumnumberof3-memberedringanglebendentries maxnaf maximumnumberofFourieranglebendparameterentries acon forceconstantparametersforharmonicanglebends acon5 forceconstantparametersfor5-ringanglebends acon4 forceconstantparametersfor4-ringanglebends acon3 forceconstantparametersfor3-ringanglebends aconf forceconstantparametersforFourieranglebends ang bondangleparametersforharmonicanglebends ang5 bondangleparametersfor5-ringanglebends ang4 bondangleparametersfor4-ringanglebends ang3 bondangleparametersfor3-ringanglebends angf phaseshiftangleandperiodicityforFourierbends ka stringofatomclassesforharmonicanglebends ka5 stringofatomclassesfor5-ringanglebends ka4 stringofatomclassesfor4-ringanglebends ka3 stringofatomclassesfor3-ringanglebends kaf stringofatomclassesforFourieranglebends KATOMS forcefieldparametersfortheatomtypes weight averageatomicmassofeachatomtype atmcls atomclassnumberforeachoftheatomtypes atmnum atomicnumberforeachoftheatomtypes ligand numberofatomstobeattachedtoeachatomtype symbol modifiedatomicsymbolforeachatomtype describe stringidentifingeachoftheatomtypes


KBONDS forcefieldparametersforbondstretching maxnb maximumnumberofbondstretchparameterentries maxnb5 maximumnumberof5-memberedringbondstretchentries maxnb4 maximumnumberof4-memberedringbondstretchentries maxnb3 maximumnumberof3-memberedringbondstretchentries maxnel maximumnumberofelectronegativitybondcorrections bcon forceconstantparametersforharmonicbondstretch bcon5 forceconstantparametersfor5-ringbondstretch bcon4 forceconstantparametersfor4-ringbondstretch bcon3 forceconstantparametersfor3-ringbondstretch blen bondlengthparametersforharmonicbondstretch blen5 bondlengthparametersfor5-ringbondstretch blen4 bondlengthparametersfor4-ringbondstretch blen3 bondlengthparametersfor3-ringbondstretch dlen electronegativitybondlengthcorrectionparameters kb stringofatomclassesforharmonicbondstretch kb5 stringofatomclassesfor5-ringbondstretch kb4 stringofatomclassesfor4-ringbondstretch kb3 stringofatomclassesfor3-ringbondstretch kel stringofatomclassesforelectronegativitycorrections KCHRGE forcefieldparametersforpartialcharges chg partialchargeparametersforeachatomtype KDIPOL forcefieldparametersforbonddipoles maxnd maximumnumberofbonddipoleparameterentries maxnd5 maximumnumberof5-memberedringdipoleentries maxnd4 maximumnumberof4-memberedringdipoleentries maxnd3 maximumnumberof3-memberedringdipoleentries dpl dipolemomentparametersforbonddipoles dpl5 dipolemomentparametersfor5-ringdipoles dpl4 dipolemomentparametersfor4-ringdipoles dpl3 dipolemomentparametersfor3-ringdipoles pos dipolepositionparametersforbonddipoles pos5 dipolepositionparametersfor5-ringdipoles pos4 dipolepositionparametersfor4-ringdipoles pos3 dipolepositionparametersfor3-ringdipoles kd stringofatomclassesforbonddipoles kd5 stringofatomclassesfor5-ringdipoles kd4 stringofatomclassesfor4-ringdipoles kd3 stringofatomclassesfor3-ringdipoles KEYS contentsofcurrentkeywordparameterfile nkey numberofnonblanklinesinthekeywordfile keyline contentsofeachindividualkeywordfileline KGEOMS parametersforthegeometricalrestraints


xpfix x-coordinatetargetforeachrestrainedposition ypfix y-coordinatetargetforeachrestrainedposition zpfix z-coordinatetargetforeachrestrainedposition pfix forceconstantandflat-wellrangeforeachposition dfix forceconstantandtargetrangeforeachdistance afix forceconstantandtargetrangeforeachangle tfix forceconstantandtargetrangeforeachtorsion gfix forceconstantandtargetrangeforeachgroupdistance chir forceconstantandtargetrangeforchiralcenters depth depthofshallowGaussianbasinrestraint width exponentialwidthcoefficientofGaussianbasin rwall radiusofsphericaldropletboundaryrestraint npfix numberofpositionrestraintstobeapplied ipfix atomnumberinvolvedineachpositionrestraint kpfix flagstousex-,y-,z-coordinatepositionrestraints ndfix numberofdistancerestraintstobeapplied idfix atomnumbersdefiningeachdistancerestraint nafix numberofanglerestraintstobeapplied iafix atomnumbersdefiningeachanglerestraint ntfix numberoftorsionalrestraintstobeapplied itfix atomnumbersdefiningeachtorsionalrestraint ngfix numberofgroupdistancerestraintstobeapplied igfix groupnumbersdefiningeachgroupdistancerestraint nchir numberofchiralityrestraintstobeapplied ichir atomnumbersdefiningeachchiralityrestraint use_basin logicalflaggoverninguseofGaussianbasin use_wall logicalflaggoverninguseofdropletboundary KHBOND forcefieldparametersforH-bondingterms maxnhb maximumnumberofhydrogenbondingpairentries radhb radiusparameterforhydrogenbondingpairs epshb welldepthparameterforhydrogenbondingpairs khb stringofatomtypesforhydrogenbondingpairs KIPROP forcefieldparametersforimproperdihedral maxndi maximumnumberofimproperdihedralparameterentries dcon forceconstantparametersforimproperdihedrals tdi idealdihedralanglevaluesforimproperdihedrals kdi stringofatomclassesforimproperdihedralangles KITORS forcefieldparametersforimpropertorsions maxnti maximumnumberofimpropertorsionparameterentries ti1 torsionalparametersforimproper1-foldrotation ti2 torsionalparametersforimproper2-foldrotation ti3 torsionalparametersforimproper3-foldrotation kti stringofatomclassesforimpropertorsionalparameters KMULTI forcefieldparametersforatomicmultipoles


maxnmp maximumnumberofatomicmultipoleparameterentries multip atomicmonopole,dipoleandquadrupolevalues mpaxis typeoflocalaxisdefinitionforatomicmultipoles kmp stringofatomtypesforatomicmultipoles KOPBND forcefieldparametersforout-of-planebend maxnopb maximumnumberofout-of-planebendingentries copb forceconstantparametersforout-of-planebending kaopb stringofatomclassesforout-of-planebending KOPDST forcefieldparametersforout-planedistance maxnopb maximumnumberofout-of-planedistanceentries copb forceconstantparametersforout-of-planedistance kaopb stringofatomclassesforout-of-planedistance KORBS forcefieldparametersforpisystemorbitals maxnpi maximumnumberofpisystembondparameterentries electron numberofpi-electronsforeachatomclass ionize ionizationpotentialforeachatomclass repulse repulsionintegralvalueforeachatomclass sslope slopeforbondstretchvs.pi-bondorder tslope slopefor2-foldtorsionvs.pi-bondorder kpi stringofatomclassesforpisystembonds KPITOR forcefieldparametersforpi-orbittorsions maxnpt maximumnumberofpi-orbitaltorsionparameterentries ptcon forceconstantparametersforpi-orbitaltorsions kpt stringofatomclassesforpi-orbitaltorsionterms KPOLR forcefieldparametersforpolarizability polr dipolepolarizabilityparametersforeachatomtype pgrp connectedtypesinpolarizationgroupofeachatomtype KSTBND forcefieldparametersforstretch-bending stbn stretch-bendingparametersforeachatomclass KSTTOR forcefieldparametersforstretch-torsions maxnbt maximumnumberofstretch-torsionparameterentries btcon forceconstantparametersforstretch-torsion kbt stringofatomclassesforbondsinstretch-torsion KTORSN forcefieldparametersfortorsionalangles


maxnt maximumnumberoftorsionalangleparameterentries maxnt5 maximumnumberof5-memberedringtorsionentries maxnt4 maximumnumberof4-memberedringtorsionentries t1 torsionalparametersforstandard1-foldrotation t2 torsionalparametersforstandard2-foldrotation t3 torsionalparametersforstandard3-foldrotation t4 torsionalparametersforstandard4-foldrotation t5 torsionalparametersforstandard5-foldrotation t6 torsionalparametersforstandard6-foldrotation t15 torsionalparametersfor1-foldrotationin5-ring t25 torsionalparametersfor2-foldrotationin5-ring t35 torsionalparametersfor3-foldrotationin5-ring t45 torsionalparametersfor4-foldrotationin5-ring t55 torsionalparametersfor5-foldrotationin5-ring t65 torsionalparametersfor6-foldrotationin5-ring t14 torsionalparametersfor1-foldrotationin4-ring t24 torsionalparametersfor2-foldrotationin4-ring t34 torsionalparametersfor3-foldrotationin4-ring t44 torsionalparametersfor4-foldrotationin4-ring t54 torsionalparametersfor5-foldrotationin4-ring t64 torsionalparametersfor6-foldrotationin4-ring kt stringofatomclassesfortorsionalangles kt5 stringofatomclassesfor5-ringtorsions kt4 stringofatomclassesfor4-ringtorsions KTRTOR forcefieldparametersfortorsion-torsions maxntt maximumnumberoftorsion-torsionparameterentries maxtgrd maximumdimensionoftorsion-torsionsplinegrid maxtgrd2 maximumnumberoftorsion-torsionsplinegridpoints ttx anglevaluesforfirsttorsionofsplinegrid tty anglevaluesforsecondtorsionofsplinegrid tbf functionvaluesatpointsonsplinegrid tbx gradientoverfirsttorsionofsplinegrid tby gradientoversecondtorsionofsplinegrid tbxy Hessiancrosscomponentsoversplinegrid tnx numberofcolumnsintorsion-torsionsplinegrid tny numberofrowsintorsion-torsionsplinegrid ktt stringoftorsion-torsionatomclasses KURYBR forcefieldparametersforUrey-Bradleyterms maxnu maximumnumberofUrey-Bradleyparameterentries ucon forceconstantparametersforUrey-Bradleyterms dst13 ideal1-3distanceparametersforUrey-Bradleyterms ku stringofatomclassesforUrey-Bradleyterms KVDWPR forcefieldparametersforspecialvdwterms maxnvp maximumnumberofspecialvanderWaalspairentries radpr radiusparameterforspecialvanderWaalspairs epspr welldepthparameterforspecialvanderWaalspairs


kvpr stringofatomclassesforspecialvanderWaalspairs KVDWS forcefieldparametersforvanderWaalsterms rad vanderWaalsradiusparameterforeachatomclass eps vanderWaalswelldepthparameterforeachatomclass rad4 vanderWaalsradiusparameterin1-4interactions eps4 vanderWaalswelldepthparameterin1-4interactions reduct vanderWaalsreductionfactorforeachatomclass LIGHT indicesformethodoflightspairneighbors nlight totalnumberofsitesformethodoflightscalculation kbx lowindexofneighborsofeachsiteinthex-sortedlist kby lowindexofneighborsofeachsiteinthey-sortedlist kbz lowindexofneighborsofeachsiteinthez-sortedlist kex highindexofneighborsofeachsiteinthex-sortedlist key highindexofneighborsofeachsiteinthey-sortedlist kez highindexofneighborsofeachsiteinthez-sortedlist locx pointerfromx-sortedlistintooriginalinteractionlist locy pointerfromy-sortedlistintooriginalinteractionlist locz pointerfromz-sortedlistintooriginalinteractionlist rgx pointerfromoriginalinteractionlistintox-sortedlist rgy pointerfromoriginalinteractionlistintoy-sortedlist rgz pointerfromoriginalinteractionlistintoz-sortedlist LINMIN parametersforlinesearchminimization stpmin minimumsteplengthincurrentlinesearchdirection stpmax maximumsteplengthincurrentlinesearchdirection cappa stringencyoflinesearch(0=tight<cappa<1=loose) slpmax projectedgradientabovewhichstepsizeisreduced angmax maximumanglebetweensearchdirectionand-gradient intmax maximumnumberofinterpolationsduringlinesearch MATH mathematicalandgeometricalconstants radian conversionfactorfromradianstodegrees pi numericalvalueofthegeometricconstant sqrtpi numericalvalueofthesquarerootofPi logten numericalvalueofthenaturallogoften sqrttwo numericalvalueofthesquarerootoftwo twosix numericalvalueofthesixthrootoftwo MDSTUF controlofmoleculardynamicstrajectory nfree totalnumberofdegreesoffreedomforasystem velsave flagtosavevelocityvectorcomponentstoafile frcsave flagtosaveforcevectorcomponentstoafile uindsave flagtosaveinducedatomicdipolestoafile integrate typeofmoleculardynamicsintegrationalgorithm


MINIMA generalparametersforminimizations fctmin valuebelowwhichfunctionisdeemedoptimized hguess initialvaluefortheH-matrixdiagonalelements maxiter maximumnumberofiterationsduringoptimization nextiter iterationnumbertouseforthefirstiteration MOLCUL individualmoleculeswithincurrentsystem molmass molecularweightforeachmoleculeinthesystem totmass totalweightofallthemoleculesinthesystem nmol totalnumberofseparatemoleculesinthesystem kmol contiguouslistoftheatomsineachmolecule imol firstandlastatomofeachmoleculeinthelist molcule numberofthemoleculetowhicheachatombelongs MOLDYN velocityandaccelerationonMDtrajectory v currentvelocityofeachatomalongthex,y,z-axes a currentaccelerationofeachatomalongx,y,z-axes aold previousaccelerationofeachatomalongx,y,z-axes MOMENT componentsofelectricmultipolemoments netchg netelectricchargeforthetotalsystem netdpl dipolemomentmagnitudeforthetotalsystem netqdp diagonalquadrupole(Qxx,Qyy,Qzz)forsystem xdpl dipolevectorx-componentintheglobalframe ydpl dipolevectory-componentintheglobalframe zdpl dipolevectorz-componentintheglobalframe xxqdp quadrupoletensorxx-componentinglobalframe xyqdp quadrupoletensorxy-componentinglobalframe xzqdp quadrupoletensorxz-componentinglobalframe yxqdp quadrupoletensoryx-componentinglobalframe yyqdp quadrupoletensoryy-componentinglobalframe yzqdp quadrupoletensoryz-componentinglobalframe zxqdp quadrupoletensorzx-componentinglobalframe zyqdp quadrupoletensorzy-componentinglobalframe zzqdp quadrupoletensorzz-componentinglobalframe MPLPOT specificsofatomicmultipolefunctions m2scale factorbywhich1-2multipoleinteractionsarescaled m3scale factorbywhich1-3multipoleinteractionsarescaled m4scale factorbywhich1-4multipoleinteractionsarescaled m5scale factorbywhich1-5multipoleinteractionsarescaled MPOLE multipolecomponentsforcurrentstructure maxpole maxcomponents(monopole=1,dipole=4,quadrupole=13)


pole multipolevaluesforeachsiteinthelocalframe rpole multipolesrotatedtotheglobalcoordinatesystem npole totalnumberofmultipolesitesinthesystem ipole numberoftheatomforeachmultipolesite polsiz numberofmutipolecomponentsateachmultipolesite zaxis numberofthez-axisdefiningatomforeachsite xaxis numberofthex-axisdefiningatomforeachsite yaxis numberofthey-axisdefiningatomforeachsite polaxe localaxistypeforeachmultipolesite MUTANT hybridatomsforfreeenergyperturbation lambda weightingofinitialstateinhybridHamiltonian nhybrid numberofatomsmutatedfrominitialtofinalstate ihybrid atomicsitesdifferingininitialandfinalstate type0 atomtypeofeachatomintheinitialstatesystem class0 atomclassofeachatomintheinitialstatesystem type1 atomtypeofeachatominthefinalstatesystem class1 atomclassofeachatominthefinalstatesystem alter trueifanatomistobemutated,falseotherwise NUCLEO parametersfornucleicacidstructure bkbone phosphatebackboneanglesforeachnucleotide glyco glycosidictorsionalangleforeachnucleotide pucker sugarpucker,either2=2'-endoor3=3'-endo dblhlx flagtomarksystemasnucleicaciddoublehelix deoxy flagtomarkdeoxyriboseorribosesugarunits hlxform helixform(A,BorZ)ofpolynucleotidestrands OMEGA dihedralsfortorsionalspacecomputations dihed currentvalueinradiansofeachdihedralangle nomega numberofdihedralanglesallowedtorotate iomega numbersoftwoatomsdefiningrotationaxis zline linenumberinZ-matrixofeachdihedralangle OPBEND out-of-planebendsinthecurrentstructure kopb forceconstantvaluesforout-of-planebending nopbend totalnumberofout-of-planebendsinthesystem iopb bondanglenumbersusedinout-of-planebending OPDIST out-of-planedistancesincurrentstructure kopd forceconstantvaluesforout-of-planedistance nopdist totalnumberofout-of-planedistancesinthesystem iopb numbersoftheatomsineachout-of-planedistance ORBITS orbitalenergiesforconjugatedpisystem


q numberofpi-electronscontributedbyeachatom w ionizationpotentialofeachpisystematom em repulsionintegralforeachpisystematom nfill numberoffilledpisystemmolecularorbitals OUTPUT controlofcoordinateoutputfileformat archive logicalflagtosavestructuresinanarchive noversion logicalflaggoverninguseoffilenameversions overwrite logicalflagtooverwriteintermediatefilesinplace cyclesave logicalflagtomarkuseofnumberedcyclefiles coordtype selectsCartesian,internal,rigidbodyornone PARAMS contentsofforcefieldparameterfile nprm numberofnonblanklinesintheparameterfile prmline contentsofeachindividualparameterfileline PATHS parametersforElberreactionpathmethod p0 reactantCartesiancoordinatesasvariables p1 productCartesiancoordinatesasvariables pmid midpointbetweenthereactantandproduct pvect vectorconnectingthereactantandproduct pstep steppercyclealongreactant-productvector pzet currentprojectiononreactant-productvector pnorm lengthofthereactant-productvector acoeff transformationmatrix'A'fromElberpaper gc gradientsofthepathconstraints PDB definitionofaProteinDataBankstructure xpdb x-coordinateofeachatomstoredinPDBformat ypdb y-coordinateofeachatomstoredinPDBformat zpdb z-coordinateofeachatomstoredinPDBformat npdb numberofatomsstoredinProteinDataBankformat resnum numberoftheresiduetowhicheachatombelongs npdb12 numberofatomsdirectlybondedtoeachCONECTatom ipdb12 atomnumbersofatomsconnectedtoeachCONECTatom pdblist listoftheProteinDataBankatomnumberofeachatom pdbtyp ProteinDataBankrecordtypeassignedtoeachatom atmnam ProteinDataBankatomnameassignedtoeachatom resnam ProteinDataBankresiduenameassignedtoeachatom PHIPSI phi-psi-omega-chianglesforaprotein phi valueofthephiangleforeachaminoacidresidue psi valueofthepsiangleforeachaminoacidresidue omega valueoftheomegaangleforeachaminoacidresidue chi valuesofthechianglesforeachaminoacidresidue chiral chiralityofeachaminoacidresidue(1=L,-1=D)


disulf residuejoinedtoeachresidueviaadisulfidelink PIORBS conjugatedsysteminthecurrentstructure norbit totalnumberofpisystemorbitalsinthesystem iorbit numbersoftheatomscontainingpisystemorbitals reorbit numberofevaluationsbetweenorbitalupdates piperp atomsdefininganormalplanetoeachorbital nbpi totalnumberofbondsaffectedbythepisystem bpi bondandpiatomnumbersforeachpisystembond ntpi totalnumberoftorsionsaffectedbythepisystem tpi torsionandpibondnumbersforeachpisystemtorsion listpi atomlistindicatingwhethereachatomhasanorbital PISTUF bondsandtorsionsinthecurrentpisystem bkpi bondstretchforceconstantsforpi-bondorderof1.0 blpi idealbondlengthvaluesforapi-bondorderof1.0 kslope rateofforceconstantdecreasewithbondorderdecrease lslope rateofbondlengthincreasewithabondorderdecrease torsp2 2-foldtorsionalenergybarrierforpi-bondorderof1.0 PITORS pi-orbitaltorsionsinthecurrentstructure kpit 2-foldpi-orbitaltorsionalforceconstants npitors totalnumberofpi-orbitaltorsionalinteractions ipit numbersoftheatomsineachpi-orbitaltorsion PME parametersforparticlemeshEwaldsummation maxfft maximumnumberofpointsalongeachFFTdirection maxorder maximumorderoftheB-splineapproximation maxtable maximumsizeoftheFFTtablearray maxgrid maximumdimensionofthePMEchargegridarray bsmod1 B-splinemodulialongthea-axisdirection bsmod2 B-splinemodulialongtheb-axisdirection bsmod3 B-splinemodulialongthec-axisdirection table intermediatearrayusedbytheFFTcalculation nfft1 numberofgridpointsalongthea-axisdirection nfft2 numberofgridpointsalongtheb-axisdirection nfft3 numberofgridpointsalongthec-axisdirection bsorder orderofthePMEB-splineapproximation POLAR polarizabilitiesandinduceddipolemoments polarity dipolepolarizabilityforeachmultipolesite(Ang**3) pdamp valueofpolarizabilitydampingfactorforeachsite uind induceddipolecomponentsateachmultipolesite uinp induceddipolesinfieldusedforenergyinteractions npolar totalnumberofpolarizablesitesinthesystem


POLGRP polarizablesitegroupconnectivitylists maxp11 maximumnumberofatomsinapolarizationgroup maxp12 maximumnumberofatomsingroups1-2toanatom maxp13 maximumnumberofatomsingroups1-3toanatom maxp14 maximumnumberofatomsingroups1-4toanatom np11 numberofatomsinpolarizationgroupofeachatom ip11 atomnumbersofatomsinsamegroupaseachatom np12 numberofatomsingroups1-2toeachatom ip12 atomnumbersofatomsingroups1-2toeachatom np13 numberofatomsingroups1-3toeachatom ip13 atomnumbersofatomsingroups1-3toeachatom np14 numberofatomsingroups1-4toeachatom ip14 atomnumbersofatomsingroups1-4toeachatom POLPOT specificsofpolarizationfunctionalform poleps induceddipoleconvergencecriterion(rmsDebyes/atom) polsor induceddipoleSORconvergenceaccelerationfactor pgamma prefactorinexponentialpolarizationdampingterm p2scale field1-2scalefactorforenergyevaluations p3scale field1-3scalefactorforenergyevaluations p4scale field1-4scalefactorforenergyevaluations p5scale field1-5scalefactorforenergyevaluations d1scale fieldintra-groupscalefactorfordirectinduced d2scale field1-2groupscalefactorfordirectinduced d3scale field1-3groupscalefactorfordirectinduced d4scale field1-4groupscalefactorfordirectinduced u1scale fieldintra-groupscalefactorformutualinduced u2scale field1-2groupscalefactorformutualinduced u3scale field1-3groupscalefactorformutualinduced u4scale field1-4groupscalefactorformutualinduced poltyp typeofpolarizationpotential(directormutual) POTENT usageofeachpotentialenergycomponent use_bond logicalflaggoverninguseofbondstretchpotential use_angle logicalflaggoverninguseofanglebendpotential use_strbnd logicalflaggoverninguseofstretch-bendpotential use_urey logicalflaggoverninguseofUrey-Bradleypotential use_angang logicalflaggoverninguseofangle-anglecrossterm use_opbend logicalflaggoverninguseofout-of-planebendterm use_opdist logicalflaggoverninguseofout-of-planedistance use_improp logicalflaggoverninguseofimproperdihedralterm use_imptor logicalflaggoverninguseofimpropertorsionterm use_tors logicalflaggoverninguseoftorsionalpotential use_pitors logicalflaggoverninguseofpi-orbitaltorsionterm use_strtor logicalflaggoverninguseofstretch-torsionterm use_tortor logicalflaggoverninguseoftorsion-torsionterm use_vdw logicalflaggoverninguseofvdwderWaalspotential use_charge logicalflaggoverninguseofcharge-chargepotential use_chgdpl logicalflaggoverninguseofcharge-dipolepotential


use_dipole logicalflaggoverninguseofdipole-dipolepotential use_mpole logicalflaggoverninguseofmultipolepotential use_polar logicalflaggoverninguseofpolarizationterm use_rxnfld logicalflaggoverninguseofreactionfieldterm use_solv logicalflaggoverninguseofsurfaceareasolvation use_gbsa logicalflaggoverninguseofGB/SAsolvationterm use_metal logicalflaggoverninguseofligandfieldterm use_geom logicalflaggoverninguseofgeometricrestraints use_extra logicalflaggoverninguseofextrapotentialterm use_orbit logicalflaggoverninguseofpisystemcomputation PRECIS valuesofmachineprecisiontolerances tiny thesmallestpositivefloatingpointvalue small thesmallestrelativefloatingpointspacing huge thelargestrelativefloatingpointspacing REFER storageofreferenceatomiccoordinateset xref referencex-coordinateforeachatominthesystem yref referencey-coordinateforeachatominthesystem zref referencez-coordinateforeachatominthesystem nref totalnumberofatomsinthereferencesystem reftyp atomtypeforeachatominthereferencesystem n12ref numberofatomsbondedtoeachreferenceatom i12ref atomnumbersofatoms1-2connectedtoeachatom refleng lengthincharactersofthereferencefilename refltitle lengthincharactersofthereferencetitlestring refnam atomnameforeachatominthereferencesystem reffile basefilenameforthereferencestructure reftitle titleusedtodescribethereferencestructure RESDUE standardbiopolymerresidueabbreviations amino three-letterabbreviationsforaminoacidstypes nuclz three-letterabbreviationsfornucleicacidstypes amino1 one-letterabbreviationsforaminoacidstypes nuclz1 one-letterabbreviationsfornucleicacidstypes RGDDYN velocitiesandmomentaforrigidbodyMD vcm currenttranslationalvelocityofeachrigidbody wcm currentangularvelocityofeachrigidbody lm currentangularmomentumofeachrigidbody linear logicalflagtomarkgroupaslinearornonlinear RIGID rigidbodycoordinatesforatomgroups xrb rigidbodyreferencex-coordinateforeachatom yrb rigidbodyreferencey-coordinateforeachatom zrb rigidbodyreferencez-coordinateforeachatom


rbc currentrigidbodycoordinatesforeachgroup use_rigid flagtomarkuseofrigidbodycoordinatesystem RING numberandlocationofsmallringstructures nring3 totalnumberof3-memberedringsinthesystem iring3 numbersoftheatomsinvolvedineach3-ring nring4 totalnumberof4-memberedringsinthesystem iring4 numbersoftheatomsinvolvedineach4-ring nring5 totalnumberof5-memberedringsinthesystem iring5 numbersoftheatomsinvolvedineach5-ring nring6 totalnumberof6-memberedringsinthesystem iring6 numbersoftheatomsinvolvedineach6-ring ROTATE moleculepartitionsforrotationofabond nrot totalnumberofatomsmovingwhenbondrotates rot atomnumbersofatomsmovingwhenbondrotates use_short logicalflaggoverninguseofshortestatomlist RXNFLD reactionfieldmatrixelementsandindices b1 firstreactionfieldmatrixelementarray b2 secondreactionfieldmatrixelementarray ijk indicesintothereactionfieldelementarrays RXNPOT specificsofreactionfieldfunctionalform rfsize radiusofreactionfieldspherecenteredatorigin rfbulkd bulkdielectricconstantofreactionfieldcontinuum rfterms numberoftermstouseinreactionfieldsummation SCALES parameterscalefactorsforoptimization scale multiplicativefactorforeachoptimizationparameter set_scale logicalflagtoshowifscalefactorshavebeenset SEQUEN sequenceinformationforabiopolymer nseq totalnumberofresiduesinbiopolymersequences nchain numberofseparatebiopolymersequencechains ichain firstandlastresidueineachbiopolymerchain seqtyp residuetypeforeachresidueinthesequence seq three-lettercodeforeachresidueinthesequence chnnam one-letteridentifierforeachsequencechain SHAKE definitionofShake/Rattleconstraints krat idealdistancevalueforrattleconstraint nrat numberofrattledistanceconstraintstoapply nratx numberofatomgroupspatialconstraintstoapply


irat atomnumbersofatomsinarattleconstraint iratx groupnumberofgroupinaspatialconstraint kratx spatialconstrainttype(1=plane,2=line,3=point) ratimage flagtouseminimumimageforrattleconstraint use_rattle logicalflagtosetuseofrattlecontraints SHUNT polynomialswitchingfunctioncoefficients off distanceatwhichthepotentialenergygoestozero off2 squareofdistanceatwhichthepotentialgoestozero cut distanceatwhichswitchingofthepotentialbegins cut2 squareofdistanceatwhichtheswitchingbegins c0 zerothordercoefficientofmultiplicativeswitch c1 firstordercoefficientofmultiplicativeswitch c2 secondordercoefficientofmultiplicativeswitch c3 thirdordercoefficientofmultiplicativeswitch c4 fourthordercoefficientofmultiplicativeswitch c5 fifthordercoefficientofmultiplicativeswitch f0 zerothordercoefficientofadditiveswitchfunction f1 firstordercoefficientofadditiveswitchfunction f2 secondordercoefficientofadditiveswitchfunction f3 thirdordercoefficientofadditiveswitchfunction f4 fourthordercoefficientofadditiveswitchfunction f5 fifthordercoefficientofadditiveswitchfunction f6 sixthordercoefficientofadditiveswitchfunction f7 seventhordercoefficientofadditiveswitchfunction SIZES parametervaluestosetarraydimensions "sizes.i"setsvaluesforcriticalarraydimensionsusedthroughoutthesoftware;theseparameterswillfixthesizeofthelargestsystemsthatcanbehandled;valuestoolargefor thecomputer'smemoryand/orswapspacetoaccomodatewillresultinpoorperformanceoroutrightfailure parameter: maximumallowednumberof: maxatm atomsinthemolecularsystem maxval atomsdirectlybondedtoanatom maxgrp user-definedgroupsofatoms maxtyp forcefieldatomtypedefinitions maxclass forcefieldatomclassdefinitions maxprm linesintheparameterfile maxkey linesinthekeywordfile maxrot bondsfortorsionalrotation maxvar optimizationvariables(vectorstorage) maxopt optimizationvariables(matrixstorage) maxhess off-diagonalHessianelements maxlight sitesformethodoflightsneighbors maxvib vibrationalfrequencies maxgeo distancegeometrypoints maxcell unitcellsinreplicatedcrystal maxring 3-,4-,or5-memberedrings maxfix geometricconstraintsandrestraints


maxbio biopolymeratomdefinitions maxres residuesinthemacromolecule maxamino aminoacidresiduetypes maxnuc nucleicacidresiduetypes maxbnd covalentbondsinmolecularsystem maxang bondanglesinmolecularsystem maxtors torsionalanglesinmolecularsystem maxbitor bitorsionsinmolecularsystem maxpi atomsinconjugatedpisystem maxpib covalentbondsinvolvingpisystem maxpit torsionalanglesinvolvingpisystem SOCKET controlparametersforsocketcommunication runtyp calculationtypeforpassingsocketinformation cstep currentoptimizationordynamicsstepnumber cdt currentdynamicscumulativesimulationtime cenergy currentpotentialenergyfromsimulation cdx currentgradientcomponentsalongthex-axis cdy currentgradientcomponentsalongthey-axis cdz currentgradientcomponentsalongthez-axis skt_init logicalflagsettotrueaftersocketinitialization use_socket logicalflaggoverninguseofexternalsockets use_gui logicalflagtoshowTINKERwasinvokedfromGUI closing logicalflagtoindicateJVMandservershutdown SOLUTE parametersforcontinuumsolvationmodels rsolv atomicradiusofeachatomforcontinuumsolvation vsolv atomicvolumeofeachatomforcontinuumsolvation asolv atomicsolvationparameters(kcal/mole/Ang**2) rborn BornradiusofeachatomforGB/SAsolvation drb solvationderivativeswithrespecttoBornradii doffset dielectricoffsettocontinuumsolvationatomicradii p1 single-atomscalefactorforanalyticalStillGB/SA p2 1-2interactionscalefactorforanalyticalStillGB/SA p3 1-3interactionscalefactorforanalyticalStillGB/SA p4 nonbondedscalefactorforanalyticalStillGB/SA p5 softcutoffparameterforanalyticalStillGB/SA gpol polarizationself-energyvaluesforeachatom shct overlapscalingfactorsforHawkins-Cramer-TruhlarGB/SA wace "omega"valuesforatomclasspairsforusewithACE s2ace "sigma^2"valuesforatomclasspairsforusewithACE uace "mu"valuesforatomclasspairsforusewithACE solvtyp solvationmodel(ASP,SASA,ONION,STILL,HCT,ACE) STODYN frictionalcoefficientsforSDtrajectory friction globalfrictionalcoefficientforexposedparticle gamma atomicfrictionalcoefficientsforeachatom use_sdarea logicalflagtousesurfaceareafrictionscaling


STRBND stretch-bendsinthecurrentstructure ksb forceconstantforstretch-bendterms nstrbnd totalnumberofstretch-bendinteractions isb angleandbondnumbersusedinstretch-bend STRTOR stretch-torsionsinthecurrentstructure kst 1-,2-and3-foldstretch-torsionforceconstants nstrtor totalnumberofstretch-torsioninteractions ist torsionandbondnumbersusedinstretch-torsion SYNTRN definitionofsynchronoustransitpath t valueofthepathcoordinate(0=reactant,1=product) pm pathcoordinateforextrapointinquadratictransit xmin1 reactantcoordinatesasarrayofoptimizationvariables xmin2 productcoordinatesasarrayofoptimizationvariables xm extracoordinatesetforquadraticsynchronoustransit TITLES titleforthecurrentmolecularsystem ltitle lengthincharactersofthenonblanktitlestring title titleusedtodescribethecurrentstructure TORPOT specificsoftorsionalfunctionalforms idihunit convertimproperdihedralenergytokcal/mole itorunit convertimpropertorsionamplitudestokcal/mole torsunit converttorsionalparameteramplitudestokcal/mole ptorunit convertpi-orbitaltorsionenergytokcal/mole storunit convertstretch-torsionenergytokcal/mole ttorunit convertstretch-torsionenergytokcal/mole TORS torsionalangleswithinthecurrentstructure tors1 1-foldamplitudeandphaseforeachtorsionalangle tors2 2-foldamplitudeandphaseforeachtorsionalangle tors3 3-foldamplitudeandphaseforeachtorsionalangle tors4 4-foldamplitudeandphaseforeachtorsionalangle tors5 5-foldamplitudeandphaseforeachtorsionalangle tors6 6-foldamplitudeandphaseforeachtorsionalangle ntors totalnumberoftorsionalanglesinthesystem itors numbersoftheatomsineachtorsionalangle TORTOR torsion-torsionsinthecurrentstructure ntortor totalnumberoftorsion-torsioninteractions itt atomsandparameterindicesfortorsion-torsion TREE potentialsmoothing&searchtreelevels


maxpss maximumnumberofpotentialsmoothinglevels etree energyreferencevalueatthetopofthetree ilevel smoothingdeformationvalueateachtreelevel nlevel numberoflevelsofpotentialsmoothingused UNITS physicalconstantsandunitconversions avogadro Avogadro'snumber(N)inparticles/mole boltzmann Boltzmannconstant(kB)ing*Ang**2/ps**2/K/mole gasconst idealgasconstant(R)inkcal/mole/K lightspd speedoflightinvacuum(c)incm/ps bohr conversionfromBohrstoAngstroms joule conversionfromcaloriestojoules evolt conversionfromHartreetoelectron-volts hartree conversionfromHartreetokcal/mole electric conversionfromelectron**2/Angtokcal/mole debye conversionfromelectron-AngtoDebyes prescon conversionfromkcal/mole/Ang**3toAtm convert conversionfromkcaltog*Ang**2/ps**2 UREY Urey-Bradleyinteractionsinthestructure uk Urey-Bradleyforceconstants(kcal/mole/Ang**2) ul ideal1-3distancevaluesinAngstroms nurey totalnumberofUrey-Bradleytermsinthesystem iury numbersoftheatomsineachUrey-Bradleyinteraction URYPOT specificsofUrey-Bradleyfunctionalform cury cubiccoefficientinUrey-Bradleypotential qury quarticcoefficientinUrey-Bradleypotential ureyunit convertUrey-Bradleyenergytokcal/mole USAGE atomsactiveduringenergycomputation nuse numberofactiveatomsusedinenergycalculation use trueifanatomisactive,falseifinactive VDW vanderWaalsparametersforcurrentstructure radmin minimumenergydistanceforeachatomclasspair epsilon welldepthparameterforeachatomclasspair radmin4 minimumenergydistancefor1-4interactionpairs epsilon4 welldepthparameterfor1-4interactionpairs radhbnd minimumenergydistanceforhydrogenbondingpairs epshbnd welldepthparameterforhydrogenbondingpairs kred valueofreductionfactorparameterforeachatom ired attachedatomfromwhichreductionfactorisapplied nvdw totalnumbervanderWaalsactivesitesinthesystem ivdw numberoftheatomforeachvanderWaalsactivesite


VDWPOT specificsofvanderWaalsfunctionalform abuck valueof"A"constantinBuckinghamvdwpotential bbuck valueof"B"constantinBuckinghamvdwpotential cbuck valueof"C"constantinBuckinghamvdwpotential ghal valueof"gamma"inbuffered14-7vdwpotential dhal valueof"delta"inbuffered14-7vdwpotential v2scale factorbywhich1-2vdwinteractionsarescaled v3scale factorbywhich1-3vdwinteractionsarescaled v4scale factorbywhich1-4vdwinteractionsarescaled v5scale factorbywhich1-5vdwinteractionsarescaled igauss coefficientsofGaussianfittovdwpotential ngauss numberofGaussiansusedinfittovdwpotential vdwtyp typeofvanderWaalspotentialenergyfunction radtyp typeofparameter(sigmaorR-min)foratomicsize radsiz atomicsizeprovidedasradiusordiameter radrule combiningruleforatomicsizeparameters epsrule combiningruleforvdwwelldepthparameters gausstyp typeofGaussianfittovanderWaalspotential VIRIAL componentsofinternalvirialtensor vir totalinternalvirialCartesiantensorcomponents WARP parametersforpotentialsurfacesmoothing m2 secondmomentoftheGDAgaussianforeachatom deform valueofthesmoothingdeformationparameter difft diffusioncoefficientfortorsionalpotential diffv diffusioncoefficientforvanderWaalspotential diffc diffusioncoefficientforcharge-chargepotential use_smooth flagtouseapotentialenergysmoothingmethod use_dem flagtousediffusionequationmethodpotential use_gda flagtousegaussiandensityannealingpotential use_tophat flagtouseanalyticaltophatsmoothedpotential use_stophat flagtouseshiftedtophatsmoothedpotential XTALS crystalstructuresforparameterfitting e0_lattice ideallatticeenergyforthecurrentcrystal moment_0 idealdipolemomentformonomerfromcrystal nxtal numberofcrystalstructurestobestored nvary numberofpotentialparameterstooptimize ivary indexforthetypesofpotentialparameters vary atomnumbersinvolvedinpotentialparameters iresid crystalstructuretowhicheachresidualrefers rsdtyp experimentalvariableforeachoftheresiduals vartyp typeofpotentialparametertobeoptimized ZCLOSE ringopeningsandclosuresforZ-matrix


nadd numberofaddedbondsbetweenZ-matrixatoms iadd numbersoftheatompairsdefiningaddedbonds ndel numberofbondsbetweenZ-matrixbondstodelete idel numbersoftheatompairsdefiningdeletedbonds ZCOORD Z-matrixinternalcoordinatedefinitions zbond bondlengthusedtodefineeachZ-matrixatom zang bondangleusedtodefineeachZ-matrixatom ztors angleortorsionusedtodefineZ-matrixatom iz definingatomnumbersforeachZ-matrixatom


11. IndexofFunction&SubroutineCalls This section contains an alphabetical cross index listing of the routines called by each TINKERprogram, subroutineand function.Routinesnotpresent in this listdonotmakecalls toanyotherportionoftheTINKERpackage. Routine ListofSourceCodeUnitscalledbythisRoutine ACTIVE GETTEXT UPCASE ADDBASE ADDBOND FINDATM JACOBI NEWATM OLDATM

OVERLAP PIALTER PIMOVE PITILT ADDSIDE ADDBASE ADDBOND FATAL FINDATM FREEUNIT

JACOBI NEWATM OLDATM OVERLAP PIALTER PIMOVE PITILT PRTSEQ VERSION

ALCHEMY ENERGY FINAL FREEUNIT GETTEXT GETXYZ

HATOM HYBRID INITIAL MECHANIC NUMERAL READXYZ UPCASE VERSION

ANALYSIS BOUNDS EANGANG3 EANGLE3 EBOND3 EBUCK3

ECHARGE3 ECHGDPL3 EDIPOLE3 EGAUSS3 EGEOM3 EHAL3 EIMPROP3 EIMPTOR3 ELJ3 EMETAL3 EMM3HB3 EMPOLE3 EOPBEND3 EOPDIST3 EPITORS3 ERXNFLD3 ESOLV3 ESTRBND3 ESTRTOR3 ETORS3 ETORTOR3 EUREY3 EXTRA3 PISCF REPLICA

ANALYZE ANALYZ4 ANALYZ6 ANALYZ8 ATOMYZE ENRGYZE

FINAL FREEUNIT GETXYZ INITIAL MECHANIC NEXTARG PARAMYZE PROPYZE READXYZ SUFFIX TRIMTEXT UPCASE VERSION

ANGLES FATAL ANNEAL BEEMAN FINAL GETTEXT GETXYZ INITIAL

MDINIT MDREST MECHANIC NEXTARG RGDSTEP SDSTEP SHAKEUP SIGMOID UPCASE VERLET

ARCHIVE ACTIVE BASEFILE FINAL FREEUNIT GETTEXT

INITIAL NEXTARG NUMERAL PRTARC PRTCAR PRTXMOL PRTXYZ READXYZ SUFFIX TRIMTEXT UPCASE VERSION


ATTACH FATAL SORT BASEFILE CONTROL GETKEY TRIMTEXT BCUINT BCUCOF BCUINT1 BCUCOF BCUINT2 BCUCOF BEEMAN GRADIENT KINETIC MDSAVE MDSTAT PRESSURE

RATTLE RATTLE2 TEMPER TEMPER2 BETAI BETACF GAMMLN BIGBLOCK CELLATOM BITORS FATAL BONDS FATAL BORN SURFATOM BSET BMAX BSSTEP FATAL MMID PZEXTR CALENDAR DATE_AND_TIME CERROR FATAL TRIMTEXT CFFTB CFFTB1 CFFTB1 PASSB PASSB2 PASSB3 PASSB4 PASSB5 CFFTF CFFTF1 CFFTF1 PASSF PASSF2 PASSF3 PASSF4 PASSF5 CFFTI CFFTI1 CHKTREE LOCALXYZ CIRPLN ANORM DOT VCROSS VNORM CLIMBER ENERGY GETREF LOCALMIN MAKEINT MAKEXYZ CLIMBRGD ENERGY LOCALRGD RIGIDXYZ


CLIMBROT ENERGY LOCALROT MAKEXYZ CLIMBTOR CHKTREE ENERGY GETREF LOCALXYZ MAKEINT

MAKEXYZ CLIMBXYZ CHKTREE ENERGY GETREF LOCALXYZ CLUSTER CUTOFFS FATAL GETNUMB GETTEXT SORTSORT3

UPCASE COMMAND GETARG UPCASE COMPRESS CERROR GETTOR CONNECT SORT CONNOLLY COMPRESS CONTACT NEIGHBOR PLACE SADDLES

TORUS VAM CONTACT ANORM CERROR PTINCY CONTROL GETTEXT UPCASE COORDS GYRATE RMSERROR CORRELATE FINAL INITIAL NEXTARG PROPERTY READBLK

TRIMTEXT CRYSTAL BIGBLOCK BOUNDS FIELD FINAL FREEUNIT

GETTEXT GETXYZ INITIAL KATOM LATTICE MOLECULE NEXTARG PRTXYZ SYMMETRY UNITCELL UPCASE VERSION

CUTOFFS GETTEXT UPCASE CYTSY CYTSYP CYTSYS DEPTH DOT VCROSS VNORM DIAGQ GETIME SETIME DIFFEQ BSSTEP GDASTAT GVALUE DIFFUSE BASEFILE FATAL FIELD FINAL FREEUNIT

INITIAL KATOM MOLECULE NEXTARG READXYZ SUFFIX UNITCELL VERSION

DISTGEOM ACTIVE ANGLES ATTACH BONDS EMBED

FATAL FINAL FREEUNIT GEODESIC GETIME GETTEXT GETXYZ GRAFIC


IMPOSE INITIAL KCHIRAL KGEOM MAKEREF NEXTARG NUMERAL PRTXYZ SETIME TORSIONS TRIFIX UPCASE VERSION

DMDUMP GRAFIC DOCUMENT FINAL FREEUNIT GETPRM GETTEXT GETWORD

INITIAL LOWCASE NEXTARG NEXTTEXT PRTPRM SORT10 SORT6 SORT7 SUFFIX TRIMTEXT UPCASE VERSION

DSTMAT GETIME GETNUMB GETTEXT INVBETA RANDOM

SETIME SORT2 TRIFIX UPCASE DYNAMIC BEEMAN FINAL GETXYZ INITIAL MDINIT

MDREST MECHANIC NEXTARG RGDSTEP SDSTEP SHAKEUP VERLET

EANGANG GROUPS IMAGE EANGANG1 GROUPS IMAGE EANGANG2 EANGANG2A GROUPS EANGANG2A IMAGE EANGANG3 GROUPS IMAGE EANGLE GROUPS IMAGE EANGLE1 GROUPS IMAGE EANGLE2 EANGLE2A EANGLE2B GROUPS EANGLE2A GROUPS IMAGE EANGLE2B IMAGE EANGLE3 GROUPS IMAGE EBOND GROUPS IMAGE EBOND1 GROUPS IMAGE EBOND2 GROUPS IMAGE EBOND3 GROUPS IMAGE EBUCK EBUCK0A EBUCK0B EBUCK0C FATAL


EBUCK0A GROUPS IMAGE SWITCH EBUCK0B GROUPS LIGHTS SWITCH EBUCK0C EGAUSS EBUCK1 EBUCK1A EBUCK1B EBUCK1C FATAL EBUCK1A GROUPS IMAGE SWITCH EBUCK1B GROUPS LIGHTS SWITCH EBUCK1C EGAUSS1 EBUCK2 EBUCK2A EBUCK2B FATAL EBUCK2A GROUPS IMAGE SWITCH EBUCK2B EGAUSS2 EBUCK3 EBUCK3A EBUCK3B EBUCK3C FATAL EBUCK3A GROUPS IMAGE SWITCH EBUCK3B GROUPS LIGHTS SWITCH EBUCK3C EGAUSS3 ECHARGE ECHARGE0A ECHARGE0B ECHARGE0C ECHARGE0D ECHARGE0E ECHARGE0A GROUPS IMAGE SWITCH ECHARGE0B GROUPS LIGHTS SWITCH ECHARGE0C ERF GROUPS ECHARGE0D EPME ERFC GROUPS IMAGE SWITCH ECHARGE0E EPME ERFC GROUPS LIGHTS SWITCH ECHARGE1 ECHARGE1A ECHARGE1B ECHARGE1C ECHARGE1D ECHARGE1A GROUPS IMAGE SWITCH ECHARGE1B GROUPS LIGHTS SWITCH ECHARGE1C ERF GROUPS


ECHARGE1D EPME1 ERFC GROUPS IMAGE SWITCH ECHARGE2 ECHARGE2A ECHARGE2B ECHARGE2C ECHARGE2A GROUPS IMAGE SWITCH ECHARGE2B ERF GROUPS ECHARGE2C ERFC GROUPS IMAGE ECHARGE3 ECHARGE3A ECHARGE3B ECHARGE3C ECHARGE3D ECHARGE3E ECHARGE3A GROUPS IMAGE SWITCH ECHARGE3B GROUPS LIGHTS SWITCH ECHARGE3C ERF GROUPS ECHARGE3D EPME3 ERFC GROUPS IMAGE SWITCH ECHARGE3E EPME3 ERFC GROUPS LIGHTS SWITCH ECHGDPL GROUPS IMAGE SWITCH ECHGDPL1 GROUPS IMAGE SWITCH ECHGDPL2 GROUPS IMAGE SWITCH ECHGDPL3 GROUPS IMAGE SWITCH EDIPOLE GROUPS IMAGE SWITCH EDIPOLE1 GROUPS IMAGE SWITCH EDIPOLE2 GROUPS IMAGE SWITCH EDIPOLE3 GROUPS IMAGE SWITCH EGAUSS EGAUSS0A EGAUSS0B EGAUSS0A GROUPS SWITCH EGAUSS0B ERF GROUPS EGAUSS1 EGAUSS1A EGAUSS1B EGAUSS1A GROUPS SWITCH EGAUSS1B ERF GROUPS


EGAUSS2 EGAUSS2A EGAUSS2B EGAUSS2A GROUPS SWITCH EGAUSS2B GROUPS EGAUSS3 EGAUSS3A EGAUSS3B EGAUSS3A GROUPS SWITCH EGAUSS3B ERF GROUPS EGBSA0A GROUPS SWITCH EGBSA0B ERF GROUPS EGBSA1A GROUPS SWITCH EGBSA1B ERF GROUPS EGBSA2A SWITCH EGBSA2B ERF EGBSA3A GROUPS SWITCH EGBSA3B ERF GROUPS EGEOM GROUPS IMAGE EGEOM1 GROUPS IMAGE EGEOM2 GROUPS IMAGE EGEOM3 GROUPS IMAGE EHAL EHAL0A EHAL0B EHAL0A GROUPS IMAGE SWITCH EHAL0B GROUPS LIGHTS SWITCH EHAL1 EHAL1A EHAL1B EHAL1A GROUPS IMAGE SWITCH EHAL1B GROUPS LIGHTS SWITCH


EHAL2 GROUPS IMAGE SWITCH EHAL3 EHAL3A EHAL3B EHAL3A GROUPS IMAGE SWITCH EHAL3B GROUPS LIGHTS SWITCH EIGEN GETIME POWER SETIME EIGENRGD DIAGQ HESSRGD EIGENROT DIAGQ HESSROT EIGENROT DIAGQ HESSROT EIGENTOR DIAGQ HESSROT EIGENXYZ DIAGQ HESSIAN EIMPROP GROUPS IMAGE EIMPROP1 GROUPS IMAGE EIMPROP2 GROUPS IMAGE EIMPROP3 GROUPS IMAGE EIMPTOR GROUPS IMAGE EIMPTOR1 GROUPS IMAGE EIMPTOR2 GROUPS IMAGE EIMPTOR3 GROUPS IMAGE ELJ ELJ0A ELJ0B ELJ0C ELJ0D ELJ0A GROUPS IMAGE SWITCH ELJ0B GROUPS LIGHTS SWITCH ELJ0C EGAUSS ELJ0D GROUPS ELJ1 ELJ1A ELJ1B ELJ1C ELJ1D ELJ1A GROUPS IMAGE SWITCH


ELJ1B GROUPS LIGHTS SWITCH ELJ1C EGAUSS1 ELJ1D GROUPS ELJ2 ELJ2A ELJ2B ELJ2A GROUPS IMAGE SWITCH ELJ2B EGAUSS2 ELJ2C GROUPS ELJ3 ELJ3A ELJ3B ELJ3C ELJ3D ELJ3A GROUPS IMAGE SWITCH ELJ3B GROUPS LIGHTS SWITCH ELJ3C EGAUSS3 ELJ3D GROUPS EMBED BNDERR CHIRER CHKSIZE COORDS DMDUMP

DSTMAT EIGEN EXPLORE FRACDIST FREEUNIT GETIME GYRATE IMPOSE LOCERR MAJORIZE METRIC NUMERAL PRTXYZ REFINE RMSERROR SETIME TORSER VDWERR

EMETAL FATAL EMETAL1 FATAL EMETAL3 EMETAL EMM3HB EMM3HB0A EMM3HB0B EMM3HB0A GROUPS IMAGE SWITCH EMM3HB0B GROUPS LIGHTS SWITCH EMM3HB1 EMM3HB1A EMM3HB1B EMM3HB1A GROUPS IMAGE SWITCH EMM3HB1B GROUPS LIGHTS SWITCH


EMM3HB2 GROUPS IMAGE SWITCH EMM3HB3 EMM3HB3A EMM3HB3B EMM3HB3A GROUPS IMAGE SWITCH EMM3HB3B GROUPS LIGHTS SWITCH EMPOLE EMPOLE0A EMPOLE0B EMPOLE0A CHKPOLE GROUPS IMAGE INDUCE ROTPOLE

SWITCH EMPOLE0B CHKPOLE EREAL ERECIP INDUCE ROTPOLE EMPOLE1 EMPOLE1A EMPOLE1B EMPOLE1A CHKPOLE GROUPS IMAGE INDUCE ROTPOLE

SWITCH TORQUE TORQUE1 EMPOLE1B CHKPOLE EREAL1 ERECIP1 INDUCE ROTPOLE

TORQUE EMPOLE2 EMPOLE2A EMPOLE2A GROUPS IMAGE SWITCH TORQUE EMPOLE3 EMPOLE3A EMPOLE3B EMPOLE3A CHKPOLE GROUPS IMAGE INDUCE ROTPOLE

SWITCH EMPOLE3B CHKPOLE EREAL3 ERECIP3 INDUCE ROTPOLE ENERGY BOUNDS EANGANG EANGLE EBOND EBUCK

ECHARGE ECHGDPL EDIPOLE EGAUSS EGEOM EHAL EIMPROP EIMPTOR ELJ EMETAL EMM3HB EMPOLE EOPBEND EOPDIST EPITORS ERXNFLD ESOLV ESTRBND ESTRTOR ETORS ETORTOR EUREY EXTRA PISCF REPLICA

ENRGYZE ANALYSIS EOPBEND GROUPS IMAGE EOPBEND1 GROUPS IMAGE


EOPBEND2 EOPBEND2A GROUPS EOPBEND2A IMAGE EOPBEND3 GROUPS IMAGE EOPDIST GROUPS IMAGE EOPDIST1 GROUPS IMAGE EOPDIST2 GROUPS IMAGE EOPDIST3 GROUPS IMAGE EPITORS GROUPS IMAGE EPITORS1 GROUPS IMAGE EPITORS2 EPITORS2A GROUPS EPITORS2A IMAGE EPITORS3 GROUPS IMAGE EPME BSPLINE FFTFRONT EPME1 BSPLINE1 FFTBACK FFTFRONT EPME3 BSPLINE FFTFRONT EPUCLC ANORM EREAL ERFC IMAGE SWITCH EREAL1 ERFC IMAGE SWITCH TORQUE TORQUE1 EREAL3 ERFC IMAGE SWITCH ERECIP1 TORQUE ERF ERFCORE ERFC ERFCORE ERFIK D1D2 RFINDEX ERFINV ERF FATAL ERXNFLD CHKPOLE ERFIK IJKPTS ROTPOLE SWITCH


ERXNFLD3 CHKPOLE ERFIK IJKPTS ROTPOLE SWITCH ESOLV BORN EGBSA0A EGBSA0B SURFACE ESOLV1 BORN BORN1 EGBSA1A EGBSA1B SURFACE ESOLV2 EGBSA2A EGBSA2B ESOLV3 BORN EGBSA3A EGBSA3B SURFACE ESTRBND GROUPS IMAGE ESTRBND1 GROUPS IMAGE ESTRBND2 GROUPS IMAGE ESTRBND3 GROUPS IMAGE ESTRTOR GROUPS IMAGE ESTRTOR1 GROUPS IMAGE ESTRTOR2 GROUPS IMAGE ESTRTOR3 GROUPS IMAGE ETORS ETORS0A ETORS0B ETORS0A GROUPS IMAGE ETORS0B GROUPS ETORS1 ETORS1A ETORS1B ETORS1A GROUPS IMAGE ETORS1B GROUPS ETORS2 ETORS2A ETORS2B ETORS2A GROUPS IMAGE ETORS2B GROUPS ETORS3 ETORS3A ETORS3B ETORS3A GROUPS IMAGE


ETORS3B GROUPS ETORTOR BCUINT GROUPS IMAGE ETORTOR1 BCUINT1 GROUPS IMAGE ETORTOR2 BCUINT2 GROUPS IMAGE ETORTOR3 BCUINT GROUPS IMAGE EUREY GROUPS IMAGE EUREY1 GROUPS IMAGE EUREY2 GROUPS IMAGE EUREY3 GROUPS IMAGE EWALDCOF ERFC EXPLORE INITERR MIDERR SIGMOID TOTERR FFTBACK CFFTB FFTFRONT CFFTF FFTSETUP CFFTI FIELD GETPRM PRMKEY FINAL SKTKILL FRACDIST DIST2 TRIMTEXT FREEUNIT FATAL GDA DIFFEQ FINAL FREEUNIT GDASTAT GETTEXT

GETXYZ INITIAL MECHANIC NEXTARG NUMERAL PRTXYZ RANDOM TNCGUPCASE VERSION

GDA1 GRADIENT HESSIAN GDA2 GRADIENT GDA3 HESSIAN GDASTAT ENERGY GYRATE OPTSAVE


GEODESIC MINPATH SORT3 GETBASE PDBATM GETIME CLOCK GETINT BASEFILE CHKXYZ CONNECT FATAL FREEUNIT

MAKEXYZ NEXTARG READINT SUFFIX VERSION

GETKEY FATAL FREEUNIT GETTEXT SUFFIX TRIMTEXT

UPCASE GETMOL2 BASEFILE FREEUNIT NEXTARG READMOL2 SUFFIX

VERSION GETNUCH PDBATM GETNUMB TRIMTEXT GETPDB BASEFILE FREEUNIT NEXTARG READPDB SUFFIX

VERSION GETPRB DIST2 DOT GETTOR VCROSS GETPRM FATAL FREEUNIT GETTEXT INITPRM NEXTARG

READPRM SUFFIX TRIMTEXT UPCASE VERSION

GETPROH PDBATM GETSEQ GETWORD TRIMTEXT UPCASE GETSEQN GETTEXT GETWORD TRIMTEXT UPCASE GETSIDE PDBATM GETTOR DIST2 GETXYZ BASEFILE FATAL FREEUNIT NEXTARG READXYZ

SUFFIX VERSION GRADIENT BOUNDS EANGANG1 EANGLE1 EBOND1 EBUCK1

ECHARGE1 ECHGDPL1 EDIPOLE1 EGAUSS1 EGEOM1 EHAL1 EIMPROP1 EIMPTOR1 ELJ1 EMETAL1 EMM3HB1 EMPOLE1 EOPBEND1 EOPDIST1 EPITORS1 ERXNFLD1 ESOLV1 ESTRBND1 ESTRTOR1 ETORS1 ETORTOR1 EUREY1 EXTRA1 PISCF REPLICA


GRADRGD GRADIENT GRADROT GRADIENT ROTLIST HANGLE NUMERAL HBOND NUMERAL HDIPOLE NUMERAL HESSIAN BORN BOUNDS CHKPOLE EANGANG2 EANGLE2

EBOND2 EBUCK2 ECHARGE2 ECHGDPL2 EDIPOLE2 EGAUSS2 EGEOM2 EHAL2 EIMPROP2 EIMPTOR2 ELJ2 EMETAL2 EMM3HB2 EMPOLE2 EOPBEND2 EOPDIST2 EPITORS2 ERXNFLD2 ESOLV2 ESTRBND2 ESTRTOR2 ETORS2 ETORTOR2 EUREY2 EXTRA2 FATAL INDUCE PISCF REPLICA ROTPOLE

HESSRGD GRADRGD RIGIDXYZ HESSROT GRADROT MAKEXYZ HIMPTOR NUMERAL HSTRTOR NUMERAL HTORS NUMERAL HYBRID HANGLE HATOM HBOND HCHARGE HDIPOLE

HIMPTOR HSTRBND HSTRTOR HTORS HVDW

IMPOSE CENTER QUATFIT RMSFIT INDUCE INDUCE0A INDUCE0B INDUCE0A FATAL GROUPS IMAGE PRTERR SWITCH INDUCE0B FATAL PRTERR UDIRECT1 UDIRECT2 UMUTUAL1

UMUTUAL2 INEDGE CERROR INERTIA JACOBI INITERR LOCERR TORSER


INITIAL COMMAND INITRES PRECISE PROMO INITROT FATAL NEXTARG ROTCHECK ROTLIST INTEDIT FIELD FINAL FREEUNIT GEOMETRY GETINT

GETWORD INITIAL MAKEXYZ NUMBER PRTINT TRIMTEXT UPCASE VERSION ZHELP ZVALUE

INTXYZ FINAL FREEUNIT GETINT INITIAL PRTXYZ

VERSION INVBETA BETAI GAMMLN INVERT FATAL IPEDGE CERROR ISPLPE CYTSY CYTSYS KANGANG GETTEXT UPCASE KANGLE GETTEXT NUMERAL UPCASE KATOM GETNUMB GETSTRING GETTEXT UPCASE KBOND GETTEXT KENEG NUMERAL UPCASE KCHARGE GETTEXT UPCASE KDIPOLE GETTEXT NUMERAL UPCASE KENEG GETTEXT NUMERAL UPCASE KEWALD EWALDCOF FATAL FFTSETUP GETTEXT MODULI

UPCASE KGEOM FATAL GEOMETRY GETTEXT GETWORD IMAGE

UPCASE KIMPROP GETTEXT NUMERAL UPCASE KIMPTOR GETTEXT NUMERAL TORPHASE UPCASE KMPOLE CHKPOLE GETTEXT NUMBER NUMERAL RANDOM

SORT3 UPCASE KOPBEND GETTEXT NUMBER NUMERAL UPCASE


KOPDIST GETTEXT NUMERAL UPCASE KORBIT GETTEXT NUMERAL UPCASE KPITORS GETTEXT NUMERAL UPCASE KPOLAR CHKPOLE GETTEXT POLARGRP UPCASE KSOLV GETTEXT GETWORD KANGLE KBOND UPCASE KSTRBND GETTEXT UPCASE KSTRTOR GETTEXT NUMERAL UPCASE KTORS GETTEXT NUMERAL TORPHASE UPCASE KTORTOR GETTEXT ISPLPE NUMERAL SORT9 UPCASE KUREY GETTEXT NUMERAL UPCASE KVDW GETTEXT NUMBER NUMERAL UPCASE LBFGS COMMENT' GETTEXT OPTSAVE SEARCH UPCASE LIGASE FINDATM LIGHTS FATAL SORT2 SORT5 LMSTEP PRECISE QRSOLVE LOCALMIN GRADIENT TNCG LOCALRGD OCVM LOCALROT OCVM LOCALXYZ TNCG MAJORIZE GETIME GYRATE RMSERROR SETIME MAKEINT ADJACENT FATAL GEOMETRY GETTEXT UPCASE MAKEPDB ATTACH FREEUNIT GETBASE GETNUCH GETPROH

GETSIDE NUMERAL PDBATM READSEQ VERSION

MAKEXYZ XYZATM MAPCHECK FREEUNIT NUMERAL PRTXYZ VERSION


MAXWELL ERFINV RANDOM MCM1 GRADIENT MCM2 HESSIAN MCMSTEP TNCG MDINIT FREEUNIT GETTEXT GETWORD GRADIENT GRPLINE

LATTICE MAXWELL MDREST NUMERAL RANVEC READDYN UPCASE VERSION

MDREST INVERT MDSAVE FATAL FREEUNIT NUMERAL OPENEND PRTDYN

PRTXYZ SKTDYN SUFFIX TRIMTEXT VERSION

MEASFN CERROR TRIPLE VCROSS VECANG VNORM MEASFP CERROR DOT VCROSS VECANG VNORM MEASFS CERROR DOT VECANG VNORM MEASPM VCROSS MECHANIC ACTIVE ANGLES ATTACH BITORS BONDS

CLUSTER CUTOFFS FATAL FIELD KANGANG KANGLE KATOM KBOND KCHARGE KDIPOLE KEWALD KGEOM KIMPROP KIMPTOR KMETAL KMPOLE KOPBEND KOPDIST KORBIT KPITORS KPOLAR KSOLV KSTRBND KSTRTOR KTORS KTORTOR KUREY KVDW LATTICE MOLECULE MUTATE ORBITAL POLYMER RINGS SMOOTH TORSIONS UNITCELL

MERGE FATAL GETREF MIDERR BNDERR CHIRER LOCERR TORSER MINIMIZ1 GRADIENT MINIMIZE FINAL FREEUNIT GETTEXT GETXYZ GRADIENT

INITIAL LBFGS MECHANIC NEXTARG PRTXYZ UPCASE VERSION


MINIROT FINAL FREEUNIT GETINT GETTEXT GRADROT INITIAL INITROT LBFGS MECHANIC NEXTARG PRTINT UPCASE VERSION

MINIROT1 GRADROT MAKEXYZ MINRIGID FINAL FREEUNIT GETTEXT GETXYZ GRADRGD

INITIAL LBFGS MECHANIC NEXTARG ORIENT PRTXYZ UPCASE VERSION

MINRIGID1 GRADRGD RIGIDXYZ MMID GVALUE MODECART CLIMBXYZ EIGENXYZ GETREF IMPOSE MAKEREF MODEROT CLIMBROT EIGENROT MAKEXYZ MODESRCH CLIMBER EIGENROT MAKEINT MAKEREF MAPCHECK MODETORS CLIMBTOR EIGENTOR GETREF IMPOSE MAKEINT

MAKEREF MODULI BSPLINE DFTMOD MOLECULE SORT SORT3 MOLUIND UFIELD MOMENTS CHKPOLE INDUCE JACOBI ROTPOLE MONTE CHKCLASH FREEUNIT GETREF GETTEXT GETXYZ

INITIAL INITROT MAKEINT MAKEREF MAKEXYZ MCMSTEP MECHANIC NEXTARG PRTXYZ RANDOM RANVEC UPCASE VERSION

MUTATE GETTEXT UPCASE NEIGHBOR CERROR DIST2 NEWATM ADDBOND XYZATM NEWTON FINAL FREEUNIT GETTEXT GETXYZ GRADIENT

INITIAL MECHANIC NEXTARG PRTXYZ TNCG UPCASE VERSION

NEWTON1 GRADIENT NEWTON2 HESSIAN


NEWTROT FINAL FREEUNIT GETINT GETTEXT GRADROT

INITIAL INITROT MECHANIC NEXTARG PRTINT TNCG UPCASE VERSION

NEWTROT1 GRADROT MAKEXYZ NEWTROT2 HESSROT MAKEXYZ NORMAL RANDOM NUCBASE OCVM ORIENT POTOFF ZATOM NUCCHAIN NUCBASE OCVM ORIENT ZATOM NUCLEIC BASEFILE CONNECT DELETE FIELD FREEUNIT

GETKEY GETSEQN INITIAL MAKEINT MAKEXYZ MOLECULE NEXTARG NUCCHAIN PRTINT PRTSEQ PRTXYZ TRIMTEXT VERSION WATSON

NUMBER TRIMTEXT OCVM GETTEXT OPTSAVE PRECISE UPCASE OLDATM ADDBOND FATAL OPTIMIZ1 GRADIENT OPTIMIZE FATAL FINAL FREEUNIT GETTEXT GETXYZ

GRADIENT INITIAL MECHANIC NEXTARG OCVM PRTXYZ UPCASE VERSION

OPTIROT FATAL FINAL FREEUNIT GETINT GETTEXT

GRADROT INITIAL INITROT MECHANIC NEXTARG OCVM PRTINT UPCASE VERSION

OPTIROT1 GRADROT MAKEXYZ OPTRIGID FATAL FINAL FREEUNIT GETTEXT GETXYZ

GRADRGD INITIAL MECHANIC NEXTARG OCVM ORIENT PRTXYZ UPCASE VERSION

OPTRIGID1 GRADRGD RIGIDXYZ OPTSAVE FATAL FREEUNIT MAKEXYZ NUMERAL OPENEND

PRTINT PRTXYZ SKTOPT SUFFIX VERSION


ORBITAL FATAL GETTEXT PIPLANE UPCASE ORIENT XYZRIGID OVERLAP SLATER PATH FINAL GETXYZ IMPOSE INITIAL INVERT

LBFGS MECHANIC NEXTARG OPTSAVE ORTHOG POTNRG

PATH1 POTNRG PATHPNT OCVM PATHSCAN PATHPNT SADDLE1 TANGENT PATHVAL IMPOSE PDBXYZ CHKXYZ DELETE FIELD FINAL FREEUNIT

GETNUMB GETPDB INITIAL LIGASE PRTXYZ RIBOSOME SORT UPCASE VERSION

PIPLANE FATAL PISCF NEWATM PITILT OLDATM PLACE CERROR DIST2 GETPRB GETTOR INEDGE POLARGRP SORT SORT8 POLARIZE FATAL GETXYZ INITIAL JACOBI MECHANIC

MOLUIND POLYMER FATAL GETTEXT IMAGE UPCASE POTNRG GRADIENT POWER RANDOM PRECOND CHOLESKY COLUMN PRESSURE LATTICE PRMKEY GETTEXT GETWORD POTOFF UPCASE


PROCHAIN GETTEXT PROSIDE UPCASE ZATOM PROJCT DOT PROPYZE GRADIENT GYRATE INERTIA MOMENTS PROSIDE FREEUNIT PRTINT PRTXYZ VERSION ZATOM PROTEIN BASEFILE CHKXYZ CONNECT DELETE FIELDFINAL

FREEUNIT GETKEY GETSEQ INITIAL MAKEINT MAKEXYZ NEXTARG PROCHAIN PRTINT PRTSEQ PRTXYZ TRIMTEXT VERSION

PRTARC VERSION PRTCAR VERSION PRTDYN ZATOM PRTERR ZATOM PRTINT VERSION PRTMOL2 NUMBER VERSION PRTPDB VERSION PRTPRM NUMBER PRTSEQ VERSION PRTXMOL VERSION PRTXYZ VERSION PSS ACTIVE FINAL GETTEXT GETXYZ IMPOSE

INITIAL INITROT LOCALXYZ MAKEINT MAKEREF MECHANIC MODECART MODETORS NEXTARG PSSWRITE SIGMOID UPCASE

PSS1 GRADIENT PSS2 HESSIAN PSSRGD1 GRADRGD RIGIDXYZ PSSRIGID FINAL FREEUNIT GETTEXT GETXYZ IMPOSE

INITIAL MAKEREF MECHANIC NEXTARG NUMERAL OCVM ORIENT PRTXYZ


RGDSRCH RIGIDXYZ SIGMOID UPCASE VERSION

PSSROT FINAL FREEUNIT GETTEXT GETXYZ IMPOSE

INITIAL INITROT MAKEREF MAKEXYZ MECHANIC MODEROT NEXTARG NUMERAL OCVM PRTXYZ UPCASE VERSION

PSSROT1 GRADROT MAKEXYZ PSSWRITE FREEUNIT NUMERAL PRTXYZ VERSION PTINCY DOT EPUCLC PROJCT ROTANG QUATFIT JACOBI RADIAL BASEFILE FATAL FINAL FREEUNIT GETTEXT

GETWORD IMAGE INITIAL LATTICE MOLECULE NEXTARG READXYZ SUFFIX UNITCELL UPCASE VERSION

RANDOM CALENDAR GETTEXT UPCASE RANVEC RANDOM RATTLE FATAL IMAGE PRTERR RATTLE2 FATAL IMAGE PRTERR READBLK FATAL FREEUNIT GETWORD NUMERAL READDYN FATAL VERSION READINT FATAL GETTEXT GETWORD NEXTTEXT TRIMTEXT

VERSION READMOL2 FATAL GETTEXT GETWORD SORT TRIMTEXT

UPCASE VERSION READPDB FATAL FIXPDB GETTEXT NEXTARG TRIMTEXT

UPCASE VERSION READPRM FATAL GETNUMB GETSTRING GETTEXT GETWORD

NUMERAL PRMKEY SORT9 TORPHASE TRIMTEXT UPCASE

READSEQ FATAL GETNUMB GETTEXT GETWORD TRIMTEXT

VERSION


READXYZ CHKXYZ FATAL GETTEXT GETWORD NEXTTEXT SORT TRIMTEXT VERSION

REFINE LBFGS REPLICA FATAL RGDSRCH CLIMBRGD EIGENRGD RIGIDXYZ RGDSTEP CHOLESKY GRADIENT KINETIC LINBODY MDSAVE

MDSTAT PRESSURE ROTRGD TEMPER2 RIBOSOME ADDBOND ADDSIDE FATAL FINDATM FREEUNIT

NEWATM OLDATM PRTSEQ VERSION RINGS ANGLES BITORS BONDS FATAL TORSIONS RMSERROR TRIMTEXT ROTANG DOT VCROSS ROTCHECK ROTLIST ROTLIST FATAL ROTPOLE ROTMAT ROTSITE SADDLE COMMENT' FATAL FINAL FREEUNIT GETTEXT

GETXYZ IMPOSE INITIAL MAKEINT MAKEXYZ MECHANIC NEXTARG PATHPNT PATHSCAN PATHVAL PRTXYZ READXYZ SADDLE1 SEARCH TANGENT UPCASE VERSION

SADDLE1 GRADIENT SADDLES CERROR IPEDGE TRIPLE SCAN ACTIVE FINAL FREEUNIT GETXYZ INITIAL

INITROT LOCALMIN MAKEINT MAPCHECK MECHANIC MODESRCH NEXTARG NUMERAL READXYZ VERSION

SCAN1 GRADIENT SCAN2 HESSIAN SDAREA SURFATOM


SDSTEP GRADIENT KINETIC MDSAVE MDSTAT PRESSURE RATTLE RATTLE2 SDTERM

SDTERM NORMAL SDAREA SETIME CLOCK SHAKEUP CHKRING GETNUMB GETTEXT GETWORD UPCASE SKTDYN CREATEUPDATE GETMONITOR NEEDUPDATE

RELEASEMONITOR SETACCELERATION SETCOORDINATES SETENERGY SETINDUCED SETTIME SETUPDATED SETVELOCITY SKTINIT

SKTINIT CREATEJVM CREATESERVERCREATESYSTEMSETATOMIC

SETATOMTYPESSETCHARGE SETCONNECTIVITY SETCOORDINATES SETFILE SETFORCEFIELD SETKEYWORD SETMASS SETNAME SETSTORY

SKTKILL DESTROYJVM DESTROYSERVER SKTDYN SKTOPT SKTOPT CREATEUPDATE GETMONITOR NEEDUPDATE

RELEASEMONITOR SETCOORDINATES SETENERGY SETGRADIENTS SETINDUCED SETSTEP SETUPDATED SKTINIT

SLATER ASET BSET CJKM POLYP SMOOTH GETTEXT GETWORD NEXTARG UPCASE SNIFFER FINAL FREEUNIT GETREF GETXYZ GRADIENT

INITIAL MAKEREF MECHANIC NEXTARG OPTSAVE PRTXYZ SNIFFER1 VERSION

SNIFFER1 GRADIENT SOAK DELETE FREEUNIT IMAGE LATTICE MAKEREF

MERGE MOLECULE READXYZ SUFFIX UNITCELL VERSION

SPACEFILL ACTIVE CONNOLLY FIELD FINAL FREEUNIT

GETTEXT GETXYZ INITIAL KATOM KVDW NEXTARG READXYZ SUFFIX UPCASE VERSION

SPECTRUM BASEFILE FREEUNIT INITIAL NEXTARG SUFFIX

VERSION


SQUARE GETTEXT LMSTEP LSQWRITE PRECISE QRFACT RSDVALUE TRUST UPCASE

SUFFIX TRIMTEXT SUPERPOSE FIELD FINAL FREEUNIT GETTEXT GETXYZ

IMPOSE INITIAL KATOM NEXTARG PRTXYZ READXYZ SUFFIX TRIMTEXT UPCASE VERSION

SURFACE FATAL SORT2 SURFATOM FATAL SORT2 SWITCH REPLICA SYBYLXYZ FINAL FREEUNIT GETMOL2 INITIAL PRTXYZ

VERSION SYMMETRY CELLATOM TANGENT PATHPNT SADDLE1 TEMPER KINETIC TEMPER2 MAXWELL RANDOM RANVEC TESTGRAD ENERGY FINAL GETTEXT GETXYZ GRADIENT

INITIAL MECHANIC NEXTARG UPCASE TESTHESS FINAL FREEUNIT GETTEXT GETXYZ GRADIENT

HESSIAN INITIAL MECHANIC NEXTARG NUMGRAD UPCASE VERSION

TESTLIGHT EBUCK EBUCK1 ECHARGE ECHARGE1 EGAUSS

EGAUSS1 EHAL EHAL1 ELJ ELJ1 EMM3HB EMM3HB1 FINAL GETIME GETXYZ INITIAL LIGHTS MECHANIC NEXTARG SETIME

TESTROT ENERGY FINAL GETINT GRADROT INITIAL

INITROT MAKEXYZ MECHANIC NEXTARG TIMER ENERGY FINAL GETIME GETTEXT GETXYZ

GRADIENT HESSIAN INITIAL MECHANIC NEXTARG SETIME UPCASE

TIMEROT ENERGY FINAL GETIME GETINT GETTEXT

GRADROT HESSROT INITIAL INITROT MECHANIC NEXTARG SETIME UPCASE


TNCG GETTEXT HMATRIX OPTSAVE PISCF SEARCH

TNSOLVE UPCASE TNSOLVE PRECOND TORSIONS FATAL TORUS CERROR GETTOR TOTERR BNDERR CHIRER LOCERR TORSER VDWERR TRIANGLE FATAL TRIPLE DOT VCROSS TRUST PRECISE RSDVALUE UDIRECT2 ERFC IMAGE SWITCH UMUTUAL2 ERFC IMAGE SWITCH UNITCELL FATAL GETTEXT GETWORD UPCASE VAM CERROR CIRPLN DEPTH DIST2 DOT

GENDOT MEASFN MEASFP MEASFS MEASPM TRIPLE VCROSS VNORM

VDWERR LIGHTS VECANG ANORM DOT TRIPLE VERLET GRADIENT KINETIC MDSAVE MDSTAT PRESSURE

RATTLE RATTLE2 TEMPER TEMPER2 VERSION LOWCASE NEXTARG TRIMTEXT VIBRATE DIAGQ FATAL FINAL FREEUNIT GETXYZ

HESSIAN INITIAL MECHANIC NEXTARG NUMERAL PRTXYZ VERSION

VIBRIGID DIAGQ FINAL GETXYZ HESSRGD INITIAL

MECHANIC ORIENT VIBROT DIAGQ FINAL GETINT HESSROT INITIAL

INITROT MECHANIC VNORM ANORM


VOLUME CONNOLLY VOLUME1 FATAL VOLUME2 FATAL WATSON ZATOM WATSON1 GRADRGD RIGIDXYZ XTALERR ENERGY XTALMOVE XTALPRM XTALFIT FINAL GETXYZ INITIAL MECHANIC NEXTARG

POTOFF SQUARE XTALPRM XTALLAT1 ENERGY LATTICE XTALMIN FINAL FREEUNIT GETXYZ GRADIENT INITIAL

LATTICE MECHANIC NEXTARG OCVMPRTXYZ TNCG VERSION XTALLAT1

XTALMOL1 GRADIENT XTALMOL2 HESSIAN XTALMOVE LATTICE XTALPRM BOUNDS LATTICE MOLECULE XYZEDIT ACTIVE BOUNDS CUTOFFS DELETE FIELDFINAL

FREEUNIT GETXYZ IMAGE INERTIA INITIAL INSERT KATOM LATTICE MAKEREF MERGE MOLECULE PRTXYZ RANDOM SOAK SORT SORT4 UNITCELL VERSION

XYZINT FINAL FREEUNIT GETTEXT GETXYZ INITIAL

MAKEINT NEXTARG PRTINT READINT UPCASE VERSION

XYZPDB FIELD FINAL FREEUNIT GETXYZ INITIAL

KATOM MAKEPDB MOLECULE PRTPDB VERSION

XYZRIGID JACOBI ROTEULER XYZSYBYL BONDS FINAL FREEUNIT GETXYZ INITIAL

PRTMOL2 VERSION ZATOM FATAL


ZVALUE MAKEXYZ TRIMTEXT


12. TestCases&Examples This section contains brief descriptions of the sample calculations found in the EXAMPLEsubdirectory of the TINKER distribution. These examples exercise several of the current TINKERprogramsandareintendedtoprovideaflavorofthecapabilitiesofthepackage. ANIONExample ComputesanestimationofthefreeenergyofhydrationofCl-anionvs.Br-anionviaa2picosecondsimulationona``hybrid''anioninaboxofwaterfollowedbyafreeenergyperturbationcalculation ARGONExample Performsaninitialenergyminimizationonaperiodicboxcontaining150argonatomsfollowedby6picoseconds of a molecular dynamics using a modified Beeman integration algorithm and aBersedsenthermostat CLUSTERExample Performsasetof10Gaussiandensityannealing(GDA)trialsonaclusterof13argonatoms inanattempttolocatetheglobalminimumenergystructure CRAMBINExample Generates a TINKER file from a PDB file, followed by a single point energy computation anddeterminationofthemolecularvolumeandsurfacearea CYCLOHEXExample First approximately locates the transition state between chair and boat cyclohexane, followed bysubsequent refinementof the transitionstateandafinalvibrationalanalysis to showthata singlenegativefrequencyisassociatedwiththesaddlepoint DIALANINEExample Findsallthelocalminimaofalaninedipeptideviaapotentialenergysurfacescanusingtorsionalmodestojumpbetweentheminima ENKEPHALINExample Producescoordinatesfromthemet-enkephalinaminoacidsequenceandphi/psiangles,followedbytruncatedNewtonenergyminimizationanddeterminationofthelowestfrequencynormalmode FORMAMIDEExample Convertstoaunitcellfromfractionalcoordinates,followedbyfullcrystalenergyminimizationanddetermination of optimal carbonyl oxygen energy parameters from a fit to lattice energy andstructure


HELIXExample Performsarigid-bodyoptimizationofthepackingoftwoidealizedpolyalaninehelicesusingonlyvanderWaalsinteractions SALTExample Converts a sodium chloride assymetric unit to the corresponding unit cell, then runs a crystalminimization starting from the initial diffraction structure using Ewald summation to model thelong-rangeelectrostaticinteractions.


13. BenchmarkResults The tables in this section provide CPU benchmarks for basic TINKER energy and derivativeevaluations, vibrational analysis and molecular dynamics. All times are in seconds and weremeasuredwithTINKERexecutablesdimensionedtomaxatmof10000andmaxhessof1000000inthesourcefilesizes.i.Allcalculationswereruntwiceinrapidsuccessiononaquietmachine.Thetimesreportedforeachbenchmarkaretheresultsfromthesecondrun.IfyouhavebuiltTINKERonan alternativemachine type and are able to run the benchmarks on the additionalmachine type,pleasesendtheresultsforinclusioninafuturelisting.

BENCHMARK#1:CalmodulinEnergyEvaluation Thesystemisanisolatedmoleculeofthe148-residueproteincalmodulinwith2264atomsusingtheAmber ff94 force field. All interactions are computedwith no use of cutoffs. Times listed are forcalculationsetupfollowedbyasingleenergy,energy/gradientandHessianevaluation. MACHINE-OS-COMPILERTYPE MHz SETUP ENERGY GRAD HESS AthlonXP2400+(RH8.0,Intel) 2000 0.13 0.28 0.60 2.96 AthlonXP2400+(RH8.0,PGI) 2000 0.16 0.31 0.70 3.60 AthlonXP2400+(RH8.0,g773.2) 2000 0.17 0.28 0.66 3.67 AthlonThunderbird(RH8.0,Intel) 1400 0.22 0.41 0.86 5.15 AthlonThunderbird(RH8.0,PGI) 1400 0.21 0.44 1.00 5.92 AthlonThunderbird(RH8.0,g773.2) 1400 0.19 0.40 0.94 5.81 AthlonClassic(RH8.0,Intel) 950 0.30 0.64 1.42 7.07 AthlonClassic(RH8.0,PGI) 950 0.30 0.69 1.65 7.96 AthlonClassic(RH8.0,g773.2) 950 0.31 0.63 1.57 7.94 CompaqEvoN610cP4(RH8.0,Intel) 2000 0.18 0.45 0.87 3.08 CompaqEvoN610cP4(RH8.0,PGI) 2000 0.22 0.44 1.06 4.27 CompaqEvoN610cP4(RH8.0,Absoft) 2000 0.17 0.52 1.06 3.95 CompaqEvoN610cP4(RH8.0,g773.2) 2000 0.19 0.41 1.07 4.41 CompaqEvoN610cP4(WinXP,CVF6.6) 2000 0.16 0.38 0.98 3.54 CompaqEvoN610cP4(WinXP,g773.2) 2000 0.16 0.40 1.08 4.45 ApplePowerMacG4(OSX10.2,Absoft) 733 0.41 2.96 5.12 17.83 ApplePowerMacG4(OSX10.2,g773.3) 733 0.37 1.98 3.79 14.48 CompaqAlphaServerDS10(Tru645.0) 466 0.35 1.33 1.93 8.40 SGIIndigoIIR10K(Irix6.5,MIPS) 195 1.17 3.49 6.35 23.03

BENCHMARK#2:CrambinCrystalEnergyEvaluation Thesystemisaunitcellofthe46-residueproteincrambincontaining2polypeptidechains,2ethanoland178watermoleculesforatotalof1360atomsusingtheOPLS-UAforcefield.PeriodicboundariesareusedwithparticlemeshEwaldforelectrostaticsanda9.0≈cutoff forvdWinteractions.Timeslistedareforcalculationsetupfollowedbyasingleenergy,energy/gradientandHessianevaluation. MACHINE-OS-COMPILERTYPE MHz SETUP ENERGY GRAD HESS AthlonXP2400+(RH8.0,Intel) 2000 0.12 0.12 0.21 0.66 AthlonXP2400+(RH8.0,PGI) 2000 0.13 0.14 0.24 0.63


AthlonXP2400+(RH8.0,g773.2) 2000 0.14 0.13 0.28 0.81 AthlonThunderbird(RH8.0,Intel) 1400 0.19 0.17 0.30 0.91 AthlonThunderbird(RH8.0,PGI) 1400 0.18 0.18 0.32 0.91 AthlonThunderbird(RH8.0,g773.2) 1400 0.17 0.17 0.38 1.11 AthlonClassic(RH8.0,Intel) 950 0.26 0.25 0.47 1.46 AthlonClassic(RH8.0,PGI) 950 0.29 0.27 0.50 1.42 AthlonClassic(RH8.0,g773.2) 950 0.27 0.27 0.56 1.70 CompaqEvoN610cP4(RH8.0,Intel) 2000 0.15 0.14 0.27 0.64 CompaqEvoN610cP4(RH8.0,PGI) 2000 0.22 0.19 0.33 0.88 CompaqEvoN610cP4(RH8.0,Absoft) 2000 0.14 0.22 0.39 0.84 CompaqEvoN610cP4(RH8.0,g773.2) 2000 0.15 0.20 0.45 1.13 CompaqEvoN610cP4(WinXP,CVF6.6) 2000 0.14 0.17 0.33 0.83 CompaqEvoN610cP4(WinXP,g773.2) 2000 0.12 0.22 0.52 1.16 ApplePowerMacG4(OSX10.2,Absoft) 733 0.32 0.58 1.09 3.11 ApplePowerMacG4(OSX10.2,g773.3) 733 0.31 0.42 0.79 2.37 CompaqAlphaServerDS10(Tru645.0) 466 0.29 0.38 0.64 1.95 SGIIndigoIIR10K(Irix6.5,MIPS) 195 0.92 0.74 1.41 3.89

BENCHMARK#3:PeptideNormalModeCalculation Thesystemisaminimumenergyconformationofa20-residuepeptidecontainingoneofeachofthestandardaminoacidsforatotalof328atomsusingtheOPLS-AAforcefieldwithoutcutoffs.ThetimereportedisforcomputationoftheHessianandcalculationofthenormalmodesoftheHessianmatrixandthevibrationfrequenciesrequiringtwoseparatematrixdiagonalizationsteps. MACHINE-OS-COMPILERTYPE MHz NORMALMODES AthlonXP2400+(RH8.0,Intel) 2000 22 AthlonXP2400+(RH8.0,PGI) 2000 26 AthlonXP2400+(RH8.0,g773.2) 2000 24 AthlonThunderbird(RH8.0,Intel) 1400 31 AthlonThunderbird(RH8.0,PGI) 1400 34 AthlonThunderbird(RH8.0,g773.2) 1400 33 AthlonClassic(RH8.0,Intel) 950 46 AthlonClassic(RH8.0,PGI) 950 51 AthlonClassic(RH8.0,g773.2) 950 48 CompaqEvoN610cP4(RH8.0,Intel) 2000 19 CompaqEvoN610cP4(RH8.0,PGI) 2000 19 CompaqEvoN610cP4(RH8.0,Absoft) 2000 20 CompaqEvoN610cP4(RH8.0,g773.2) 2000 19 CompaqEvoN610cP4(WinXP,CVF6.6) 2000 19 CompaqEvoN610cP4(WinXP,g773.2) 2000 20 ApplePowerMacG4(OSX10.2,Absoft) 733 67 ApplePowerMacG4(OSX10.2,g773.3) 733 62 CompaqAlphaServerDS10(Tru645.0) 466 39 SGIIndigoIIR10K(Irix6.5,MIPS) 195 144

BENCHMARK#4:TIP3PWaterBoxMolecularDynamics


The system consists of 216 rigidTIP3Pwatermolecules in a 18.643≈ periodic box, 9.0 ≈ shiftedenergyswitchcutoffsfornonbondedinteractions.Thetimereportedisfor1000dynamicsstepsof1.0fseachusingthemodifiedBeemanintegratorandRattleconstraintsonallbondlengths. MACHINE-OS-COMPILERTYPE MHz DYNAMICS AthlonXP2400+(RH8.0,Intel) 2000 37 AthlonXP2400+(RH8.0,PGI) 2000 34 AthlonXP2400+(RH8.0,g773.2) 2000 45 AthlonThunderbird(RH8.0,Intel) 1400 52 AthlonThunderbird(RH8.0,PGI) 1400 47 AthlonThunderbird(RH8.0,g773.2) 1400 63 AthlonClassic(RH8.0,Intel) 950 77 AthlonClassic(RH8.0,PGI) 950 71 AthlonClassic(RH8.0,g773.2) 950 96 CompaqEvoN610cP4(RH8.0,Intel) 2000 53 CompaqEvoN610cP4(RH8.0,PGI) 2000 54 CompaqEvoN610cP4(RH8.0,Absoft) 2000 55 CompaqEvoN610cP4(RH8.0,g773.2) 2000 91 CompaqEvoN610cP4(WinXP,CVF6.6) 2000 63 CompaqEvoN610cP4(WinXP,g773.2) 2000 94 ApplePowerMacG4(OSX10.2,Absoft) 733 209 ApplePowerMacG4(OSX10.2,g773.3) 733 170 CompaqAlphaServerDS10(Tru645.0) 466 106 SGIIndigoIIR10K(Irix6.5,MIPS) 195 280

BENCHMARK#5:TINKERWaterBoxMolecularDynamics The system consists of 216 AMOEBA flexible polarizable atomic multipole water molecules in a18.643≈periodicboxusingregularEwaldsummation for theelectrostaticsanda12.0≈switchedcutoff for vdW interactions. The time reported is for 100dynamics steps of 1.0 fs each using themodifiedBeemanintegratorand0.01Debyermsconvergenceforinduceddipolemoments. MACHINE-OS-COMPILERTYPE MHz DYNAMICS AthlonXP2400+(RH8.0,Intel) 2000 108 AthlonXP2400+(RH8.0,PGI) 2000 104 AthlonXP2400+(RH8.0,g773.2) 2000 128 AthlonThunderbird(RH8.0,Intel) 1400 165 AthlonThunderbird(RH8.0,PGI) 1400 158 AthlonThunderbird(RH8.0,g773.2) 1400 183 AthlonClassic(RH8.0,Intel) 950 282 AthlonClassic(RH8.0,PGI) 950 261 AthlonClassic(RH8.0,g773.2) 950 307 CompaqEvoN610cP4(RH8.0,Intel) 2000 156 CompaqEvoN610cP4(RH8.0,PGI) 2000 191 CompaqEvoN610cP4(RH8.0,Absoft) 2000 226 CompaqEvoN610cP4(RH8.0,g773.2) 2000 243 CompaqEvoN610cP4(WinXP,CVF6.6) 2000 176 CompaqEvoN610cP4(WinXP,g773.2) 2000 263 ApplePowerMacG4(OSX10.2,Absoft) 733 680


ApplePowerMacG4(OSX10.2,g773.3) 733 479 CompaqAlphaServerDS10(Tru645.0) 466 358 SGIIndigoIIR10K(Irix6.5,MIPS) 195 868


14. Collaborators&Acknowledgments TheTINKERpackagehasdevelopedoveraperiodofmanyyears,veryslowlyduringthelate-1980s,andmorerapidlysincethemid-1990sinJayPonder'sresearchgroupattheWashingtonUniversitySchoolofMedicineinSaintLouis.Manypeoplehaveplayedsignificantrolesinthedevelopmentofthepackageintoitscurrentform.Themajorcontributorsarelistedbelow: StewRubenstein coordinateinterconversions;originaloptimizationmethods andtorsionalanglemanipulation CraigKundrot molecularsurfacearea&volumeandtheirderivatives ShawnHuston originalAMBER/OPLSimplementation;freeenergy calculations;timecorrelationfunctions MikeDudek initialmultipolemodelsforpeptidesandproteins Yong"Mike"Kong multipoleelectrostatics;dipolepolarization;reactionfield treatment;TINKERwatermodel ReeceHart potentialsmoothingmethodology;Scheraga'sDEM, Straub'sGDAandextensions MikeHodsdon extensionoftheTINKERdistgeomprogramandits applicationtoNMRNOEstructuredetermination RohitPappu potentialsmoothingmethodologyandPSSalgorithms; rigidbodyoptimization;GB/SAsolvationderivatives WijnandMooij MM3directionalhydrogenbondingterm;crystallattice minimizationcode GeraldLoeffler stochastic/Langevindynamicsimplementation MarinaVorobieva nucleicacidbuildingmoduleandparametertranslation NinaSokolova PeterBagossi AMOEBAforcefieldparametersforalkanesanddiatomics PengyuRen Ewaldsummationforpolarizableatomicmultipoles; AMOEBAforcefieldforwater,organicsandpeptides AndersCarlsson originalligandfieldpotentialenergytermfortransitionmetals AndreyKutepov integratorforrigid-bodydynamicstrajectories TomDarden ParticleMeshEwald(PME)code,anddevelopmentofPME fortheAMOEBAforcefield


AlanGrossfield MonteCarlominimization;tophatpotentialsmoothing MichaelSchnieders ForceFieldExplorerGUIforTINKER;neighborlistsfor nonbondedinteractions ChuanjieWu solvationfreeenergycalculations;AMOEBAnucleicacidforce field;parameterizationtoolsforTINKER JustinXiang angularoverlapandvalencebondpotentialmodelsfor transitionmetalsDavidGohara OpenMPparallelizationofenergytermsincludingPME, andparallelneighborlists It iscritically importantthatTINKER'sdistributedforcefieldparametersetsexactlyreproducetheintent of the original force field authors.Wewould like to thank JulianTirado-Rives (OPLS-AA),Alex MacKerell (CHARMM27),Wilfred van Gunsteren (GROMOS), and Adrian Roitberg andCarlosSimmerling (AMBER)for theirhelp in testingTINKER's resultsagainst thosegivenby theauthenticprogramsandparametersets.LouAllinger providedupdatedparameters forMM2andMM3 on several occasions. His very successful methods provided the original inspiration for thedevelopmentofTINKER. Still other workers have devoted considerable time in developing code that will hopefully beincorporated into future TINKER versions; for example, Jim Kress (UFF implementation) andMichael Sheets (numerous code optimizations, thermodynamic integration). Finally, we wish tothank the many users of the TINKER package for their suggestions and comments, praise andcriticism,whichhaveresultedinavarietyofimprovements.


15. References&SuggestedReading Thissectioncontainsalistofthereferencestogeneraltheory,algorithmsandimplementationdetailswhichhavebeenofuseduringthedevelopmentoftheTINKERpackage.MethodsdescribedinsomeofthereferenceshavebeenimplementedindetailwithintheTINKERsourcecode.Otherreferencescontainusefulbackground informationalthough thealgorithms themselvesarenowobsolete.Stillother papers contain ideas or extensions planned for future inclusion in TINKER. References forspecificforcefieldparametersetsareprovidedinanearliersectionofthisUser'sGuide.Thislistisheavily skewed toward biomolecules in general and proteins in particular. This bias reflects ourgroup'smajor interests; however an attempt hasbeenmade to includemethodswhich should begenerallyapplicable. PARTIALLISTOFMOLECULARMECHANICSSOFTWAREPACKAGES AMBER PeterKollman,UniversityofCalifornia,SanFrancisco AMMP RobHarrison,ThomasJeffersonUniversity,Philadelphia ARGOS AndyMcCammon,UniversityofCalifornia,SanDiego BOSS WilliamJorgensen,YaleUniversity BRUGEL ShoshonaWodak,FreeUniversityofBrussels CFF ShneiorLifson,WeizmannInstitute CHARMM MartinKarplus,HarvardUniversity CHARMM/GEMM BernardBrooks,NationalInstitutesofHealth,Bethesda DELPHI BastianvandeGraaf,DelftUniversityofTechnology DISCOVER MolecularSimulationsInc.,SanDiego DL_POLY W.Smith&T.Forester,CCP5,DaresburyLaboratory ECEPP HaroldScheraga,CornellUniversity ENCAD MichaelLevitt,StanfordUniversity FANTOM WernerBraun,UniversityofTexas,Galveston FEDER/2 NobuhiroGo,KyotoUniversity GROMACS HermanBerendsen,UniversityofGroningen GROMOS WilfredvanGunsteren,BIOMOSandETH,Zurich IMPACT RonaldLevy,RutgersUniversity MACROMODEL Schodinger,Inc.,JerseyCity,NewJersey MM2/MM3/MM4 N.LouAllinger,UniversityofGeorgia MMC CliffDykstra,IndianaUniv.≠PurdueUniv.atIndianapolis MMFF TomHalgren,MerckResearchLaboratories,Rahway MMTK KonradHinsen,Inst.ofStructuralBiology,Grenoble MOIL RonElber,CornellUniversity MOLARIS AriehWarshal,UniversityofSouthernCalifornia MOLDY KeithRefson,OxfordUniversity MOSCITO DietmarPaschek&AlfonsGeiger,Universit‰tDortmund NAMD KlausSchulten,UniversityofIllinois,Urbana OOMPAA AndyMcCammon,UniversityofCalifornia,SanDiego ORAL KarelZimmerman,INRA,Jouy-en-Josas,France ORIENT AnthonyStone,CambridgeUniversity PCMODEL KevinGilbert,SerenaSoftware,Bloomington,Indiana PEFF JanDillen,UniversityofPretoria,SouthAfrica Q Johan≈qvist,UppsalaUniversity SIBFA NohadGresh,INSERM,CNRS,Paris SIGMA JanHermans,UniversityofNorthCarolina SPASIBA GerardVergoten,UniversitÈdeLille SPASMS DavidSpellmeyerandtheKollmanGroup,UCSF


TINKER JayPonder,WashingtonUniversity,St.Louis XPLOR/CNS AxelBr¸nger,StanfordUniversity YAMMP StephenHarvey,UniversityofAlabama,Birmingham YASP FlorianMueller-Plathe,ETHZentrum,Zurich YETI AngeloVedani,Biografik-Labor3R,Basel AMBER D. A Pearlman, D. A. Case, J.W. Caldwell,W. S. Ross, T. E. Cheatham III, S. DeBolt, D.Ferguson,G.SeibelandP.Kollman,AMBER,aPackageofComputerProgramsforApplyingMolecularMechanics,NormalModeAnalysis,MolecularDynamicsandFreeEnergyCalculationstoSimulatetheStructuralandEnergeticPropertiesofMolecules,Comp.Phys.Commun.,91,1-41(1995) ARGOS T.P.Straatsmaand J.A.McCammon,ARGOS,aVectorizedGeneralMolecularDynamicsProgram,J.Comput.Chem.,11,943-951(1990) CHARMMB.R.Brooks,R.E.Bruccoleri,B.D.Olafson,D.J.States,S.SwaminathanandM.Karplus,CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, J.Comput.Chem.,4,187-217(1983) ENCAD M. Levitt, M. Hirshberg, R. Sharon and V. Daggett, Potential Energy Function andParameters for Simulations for theMolecularDynamics of Proteins andNucleicAcids in Solution,Comp.Phys.Commun.,91,215-231(1995) FANTOMT.Schaumann,W.BraunandK.Wurtrich,TheProgramFANTOMforEnergyRefinementof Polypeptides and Proteins Using a Newton-Raphson Minimizer in Torsion Angle Space,Biopolymers,29,679-694(1990) FEDER/2 H.Wako,S.Endo,K.NagayamaandN.Go,FEDER/2:ProgramforStaticandDynamicConformationalEnergyAnalysisofMacro-moleculesinDihedralAngleSpace,Comp.Phys.Commun.,91,233-251(1995) GROMACS E. Lindahl, B. Hess and D. van der Spoel, GROMACS 3.0: A Package for MolecularSimulationandTrajectoryAnalysis,J.Mol.Mol.,7,306-317(2001) GROMOS W.R.P.Scott,P.H.Hunenberger , I.G.Tironi,A.E.Mark,S.R.Billeter,J.Fennen,A.E.Torda, T. Huber, P. Kruger,W. F. van Gunsteren, The GROMOS Biomolecular Simulation ProgramPackage,J.Phys.Chem.A,103,3596-3607(1999) IMPACT D.B.Kitchen,F.Hirata, J.D.Westbrook,R.Levy,D.KofkeandM.Yarmush,ConservingEnergyduringMolecularDynamicsSimulationsofWater,Proteins,andProteinsinWater,J.Comput.Chem.,10,1169-1180(1990) MACROMODEL F.Mahamadi,N.G. J.Richards,W.C.Guida,R.Liskamp,M.Lipton,C.Caufield,G.Chang, T. Hendrickson andW. C. Still, MacroModel≠An Integrated Software System for ModelingOrganicandBioorganicMoleculesUsingMolecularMechanics,J.Comput.Chem.,11,440-467(1990) MM2 N.L.Allinger,ConformationalAnalysis.130.MM2.AHydrocarbonForceFieldUtilizingV1andV2TorsionalTerms,J.Am.Chem.Soc.,99,8127-8134(1977) MM3 N. L. Allinger, Y. H. Yuh and J.-H. Lii, Molecular Mechanics. The MM3 Force Field forHydrocarbons,J.Am.Chem.Soc.,111,8551-8566(1989)


MM4 N. L. Allinger, K. Chen and J.-H. Lii, An Improved Force Field (MM4) for SaturatedHydrocarbons,J.Comput.Chem.,17,642-668(1996) MMCC.E.Dykstra,MolecularMechanicsforWeaklyInteractingAssembliesofRareGasAtomsandSmallMolecules,J.Am.Chem.Soc.,111,6168-6174(1989) MMFF T. A.Halgren,MerckMolecularForceField. I. Basis, Form, Scope,Parameterization, andPerformanceofMMFF94,J.Comput.Chem.,17,490-516(1996) MOILR.Elber,A.Roitberg,C.Simmerling,R.Goldstein,H.Li,G.Verkhiver,C.Keasar,J.ZhangandA.Ulitsky,MOIL:AProgram for Simulations ofMacromolecules,Comp.Phys. Commun.,91, 159-189(1995) MOSCITOSeethewebsiteathttp:/ganter.chemie.uni-dortmund.de/~pas/moscito.html NAMDL.KalÈ,R.Skeel,M.Bhandarkar,R.Brunner,A.Gursoy,N.Krawetz,J.Phillips,A.Shinozaki,K. Varadarajan and K. Schulten, NAMD2: Greater Scalability for Parallel Molecular Dynamics, J.Comput.Phys.,151,283-312(1999) OOMPAA G. A. Huber and J. A. McCammon, OOMPAA≠Object-oriented Model for ProbingAssemblagesofAtoms,J.Comput.Phys.,151,264-282(1999) ORALK.Zimmermann,ORAL:AllPurposeMolecularMechanicsSimulatorandEnergyMinimizer,J.Comput.Chem.,12,310-319(1991) PCMODELSeethewebsiteathttp:/www.serenasoft.com PEFF J.L.M.Dillen,PEFF:AProgramfortheDevelopmentofEmpiricalForceFields,J.Comput.Chem.,13,257-267(1992) QSeethewebsiteathttp://aqvist.bmc.uu.se/Q SIBFA N.Gresh,Inter-andIntramolecularInteractions.InceptionandRefinementsoftheSIBFA,MolecularMechanics(SMM)Procedure,aSeparable,PolarizableMethodologyGroundedonabInitioSCF/MP2Computations.ExamplesofApplicationstoMolecularRecognitionProblems,J.Chim.Phys.PCB,94,1365-1416(1997) SIGMASeethewebsiteathttp://femto.med.unc.edu/SIGMA SPASIBAP.DerreumauxandG.Vergoten,ANewSpectroscopicMolecularMechanicsForce-Field-ParametersForProteins,J.Chem.Phys.,102,8586-8605(1995) TINKERSeethewebsiteathttp://dasher.wustl.edu/tinker YAMMP R.K.-Z.TanandS.C.Harvey,Yammp:DevelopmentofaMolecularMechanicsProgramUsingtheModularProgrammingMethod,J.Comput.Chem.,14,455-470(1993) YETI A.Vedani,YETI: An InteractiveMolecularMechanicsProgram forSmall-MoleculeProteinComplexes,J.Comput.Chem.,9,269-280(1988)


MOLECULARMECHANICS U.BurkertandN.L.Allinger,MolecularMechanics,AmericanChemicalSociety,Washington,D.C.,1982 P.CombaandT.W.Hambley,MolecularModelingofInorganicCompounds,2ndEd.,Wiley-VCH,NewYork,2001 K.Machida,Principles ofMolecularMechanics, Kodansha/JohnWiley& Sons, Tokyo/NewYork,1999 A.K.RappÈandC. J.Casewit,MolecularMechanicsacrossChemistry,UniversityScienceBooks,Sausalito,CA,1997 K. Rasmussen, Potential Energy Functions in Conformational Analysis (Lecture Notes inChemistry,Vol.27),Springer-Verlag,Berlin,1985 COMPUTERSIMULATIONMETHODS M.P. AllenandD. J.Tildesley,ComputerSimulationof Liquids, OxfordUniversity Press,Oxford,1987 C.J.Cramer,EssentialsofComputationalChemistry:TheoriesandModels,JohnWileyandSons,NewYork,2002 M. J. Field,A Practical Introduction to the Simulation ofMolecular Systems, Cambridge Univ.Press,Cambridge,1999 D.FrankelandB.Smit,UnderstandingMolecularSimulation:FromAlgorithmstoApplications,2ndEd.,AcademicPress,SanDiego,CA,2001 J.M.Haile,MolecularDynamicsSimulation:ElementaryMethods,JohnWileyandSons,NewYork,1992 F.Jensen,IntroductiontoComputationalChemistry,JohnWileyandSons,NewYork,1998 A.R.Leach,MolecularModelling:PrinciplesandApplications,2ndEd.,AddisonWesleyLongman,Essex,England,2001 D.C.Rapaport,TheArtofMolecularDynamicsSimulation,2ndEd.,CambridgeUniversityPress,Cambridge,2004 T.Schlick,MolecularModelingandSimulation,Springer-Verlag,NewYork,2002 MODELINGOFBIOLOGICALMACROMOLECULES O.M.Becker,A.D.MacKerell,Jr.,B.RouxandM.Watanabe,Eds.,ComputationalBiochemistryandBiophysics,MarcelDekker,NewYork,2001


C. L. Brooks III,M.Karplus andB.M. Pettitt,Proteins:ATheoreticalPerspectiveofDynamics,Structure,andThermodynamics,JohnWileyandSons,NewYork,1988 V. Daggett, Ed., Protein Simulations (Advances in Protein Chemistry, Vol. 66), AcademicPress/Elsevier,NewYork,2003 J. A.McCammon and S.Harvey,Dynamics ofProteins and Nucleic Acids, Cambridge UniversityPress,Cambridge,1987 W. F. van Gunsteren, P. K. Weiner and A. J. Wilkinson, Computer Simulation of BiomolecularSystems,Vol.1-3,KluwerAcademicPublishers,Dordrecht,1989-1997 CONJUGATEGRADIENTANDQUASI-NEWTONOPTIMIZATION J.NocedalandS.J.Wright,NumericalOptimization,Springer-Verlag,NewYork,1999 S.G.NashandA.Sofer,LinearandNonlinearProgramming,McGraw-Hill,NewYork,1996 R.Fletcher,PracticalMethodsofOptimization,JohnWiley&SonsLtd.,Chichester,1987 D. G. Luenberger, Linear and Nonlinear Programming, 2nd Ed., Addison-Wesley, Reading, MA,1984 P.E.Gill,W.MurrayandM.H.Wright,PracticalOptimization,AcademicPress,NewYork,1981 J.Nocedal,UpdatingQuasi-NewtonMatriceswithLimitedStorage,Math.Comp.,773-782(1980) S. J.Watowich, E. S. Meyer, R. Hagstrom and R. Josephs, A Stable, Rapidly Converging ConjugateGradientMethodforEnergyMinimization,J.Comput.Chem.,9,650-661(1988) W.C.Davidon,OptimallyConditionedOptimizationAlgorithmswithoutLineSearches,Math.Prog.,9,1-30(1975) TRUNCATEDNEWTONOPTIMIZATION J.W.PonderandF.M.Richards,AnEfficientNewton-likeMethod forMolecularMechanicsEnergyMinimizationofLargeMolecules,J.Comput.Chem.,8,1016-1024(1987) R. S. Dembo and T. Steihaug, Truncated-Newton Algorithms for Large-Scale UnconstrainedOptimization,Math.Prog.,26,190-212(1983) S.C.EisenstatandH.F.Walker,ChoosingtheForcingTermsinanInexactNewtonMethod,SIAMJ.Sci.Comput.,17,16-32(1996) T.SchlickandM.Overton,APowerfulTruncatedNewtonMethodforPotentialEnergyMinimization,J.Comput.Chem.,8,1025-1039(1987) D. S. Kershaw, The Incomplete Cholesky-Conjugate Gradient Method for the Iterative Solution ofSystemsofLinearEquations,J.Comput.Phys.,26,43-65(1978)


T.A.Manteuffel,AnIncompleteFactorizationTechniqueforPositiveDefiniteLinearSystems,Math.Comp.,34,473-497(1980) P.Derreumaux,G.ZhangandT.SchlickandB.R.Brooks,ATruncatedNewtonMinimizerAdaptedforCHARMMandBiomolecularApplications,J.Comput.Chem.,15,532-552(1994) I.S.Duff,A.M.ErismanandJ.K.Reid,DirectMethodsforSparseMatrices,OxfordUniversityPress,Oxford,1986 POTENTIALENERGYSMOOTHING R. V. Pappu, R. K. Hart and J.W. Ponder, Analysis andApplication of Potential Energy SmoothingMethodsforGlobalOptimization,J.Phys.Chem.B,102,9725-9742(1998) L. Piela, J. Kostrowicki and H. A. Scheraga, The Multiple-Minima Problem in the ConformationalAnalysisofMolecules.DeformationofthePotentialEnergyHypersurfacebytheDiffusionEquationMethod,J.Phys.Chem.,93,3339-3346(1989) J.MaandJ.E.Straub,SimulatedAnnealingUsingtheClassicalDensityDistribution,J.Chem.Phys.,101,533-541(1994) C.TsooandC.L.Brooks,ClusterStructureDeterminationUsingGaussianDensityDistributionGlobalMinimizationMethods,J.Chem.Phys.,101,6405-6411(1994) S.Nakamura,H.Hirose,M. Ikeguchiand J.Doi,ConformationalEnergyMinimizationUsingaTwo-StageMethod,J.Phys.Chem.,99,8374-8378(1995) T. Huber, A. E. Torda and W. F. van Gunsteren, Structure Optimization Combining Soft-CoreInteractionFunctions,theDiffusionEquationMethod,andMolecularDynamics,J.Phys.Chem.A,101,5926-5930(1997) S. Schelstraete and H. Verschelde, Finding Minimum-Energy Configurations of Lennard-JonesClustersUsinganEffectivePotential,J.Phys.Chem.A,101,310-315(1998) I.AndricioaeiandJ.E.Straub,GlobalOptimizationUsingBadDerivatives:Derivative-FreeMethodforMolecularEnergyMinimization,J.Comput.Chem.,19,1445-1455(1998) L. Piela, Search for the Most Stable Structures on Potential Energy Surfaces, Coll. Czech. Chem.Commun.,63,1368-1380(1998) ``SNIFFER''GLOBALOPTIMIZATION A.O.Griewank,GeneralizedDescentforGlobalOptimization,J.Opt.Theor.Appl.,34,11-39(1981) R.A.R.ButlerandE.E.Slaminka,AnEvaluationoftheSnifferGlobalOptimizationAlgorithmUsingStandardTestFunctions,J.Comput.Phys.,99,28-32(1993) J. W. Rogers and R. A. Donnelly, Potential Transformation Methods for Large-Scale GlobalOptimization,SIAMJ.Optim.,5,871-891(1995)


INTEGRATIONMETHODSFORMOLECULARDYNAMICS D.Beeman,SomeMultistepMethodsforUseinMolecularDynamicsCalculations,J.Comput.Phys.,20,130-139(1976) M.LevittandH.Meirovitch,IntegratingtheEquationsofMotion,J.Mol.Biol.,168,617-620(1983) J.Aqvist,W.F.vanGunsteren,M.LeijonmarckandO.Tapia,AMolecularDynamicsStudyof theC-TerminalFragmentoftheL7/L12RibosomalProtein,J.Mol.Biol.,183,461-477(1985) W.C.Swope,H.C.Andersen,P.H.BerensandK.R.Wilson,AComputerSimulationMethodfortheCalculationofEquilibriumConstantsfortheFormationofPhysicalClustersofMolecules:ApplicationtoSmallWaterClusters,J.Chem.Phys.,76,637-649(1982) CONSTRAINTDYNAMICS W.F.vanGunsterenandH.J.C.Berendsen,AlgorithmsforMacromolecularDynamicsandConstraintDynamics,Mol.Phys.,34,1311-1327(1977) G. Ciccotti, M. Ferrario and J.-P. Ryckaert, Molecular Dynamics of Rigid Systems in CartesianCoordinates:AGeneralFormulation,Mol.Phys.,47,1253-1264(1982) H. C. Andersen, Rattle: A ``Velocity'' Version of the Shake Algorithm for Molecular DynamicsCalculations,J.Comput.Phys.,52,24-34(1983) R.Kutteh,RATTLERecipeforGeneralHolonomicConstraints:AngleandTorsionConstraints,CCP5Newsletter, 46, 9-17 (1998) [available from the web site athttp://www.dl.ac.uk/CCP/CCP5/newsletter_index.html] B.J.Palmer,DirectApplicationofSHAKEtotheVelocityVerletAlgorithm,J.Comput.Phys.,104,470-472(1993) S.MiyamotoandP.A.Kollman,SETTLE:AnAnalyticalVersionoftheSHAKEandRATTLEAlgorithmforRigidWaterModels,J.Comput.Chem.,13,952-962(1992) B.Hess,H.Bekker,H. J.C.Berendsenand J.G.E.M.Fraaije,LINCS:ALinearConstraintSolver forMolecularSimulations,J.Comput.Chem.,18,1463-1472(1997) J. T. Slusher andP. T.Cummings,Non-IterativeConstraintDynamics usingVelocity-Explicit VerletMethods,Mol.Simul.,18,213-224(1996) LANGEVIN,BROWNIANANDSTOCHASTICDYNAMICS M.P.Allen,BrownianDynamicsSimulationofaChemicalReactioninSolution,Mol.Phys.,40,1073-1087(1980) W.F.vanGunsterenandH.J.C.Berendsen,AlgorithmsforBrownianDynamics,Mol.Phys.,45,637-647(1982)


F.GuarnieriandW.C.Still,ARapidlyConvergentSimulationMethod:MixedMonteCarlo/StochasticDynamics,J.Comput.Chem.,15,1302-1310(1994) M.G.PaterliniandD.M.Ferguson,ConstantTemperatureSimulationsusingtheLangevinEquationwithVelocityVerletIntegration,Chem.Phys.,236,243-252(1998) CONSTANTTEMPERATUREANDPRESSUREDYNAMICS H.J.C.Berendsen,J.P.M.Postma,W.F.vanGunsteren,A.DiNolaandJ.R.Haak,MolecularDynamicswithCouplingtoanExternalBath,J.Chem.Phys.,81,3684-3690(1984) W.G.Hoover,CanonicalDynamics:EquilibriumPhase-spaceDistributions,Phys.Rev.A,31,1695-1697(1985) J. J. Morales, S. Toxvaerd and L. F. Rull, Computer Simulation of a Phase Transition at ConstantTemperatureandPressure,Phys.Rev.A,34,1495-1498(1986) B. R. Brooks, Algorithms forMolecular Dynamics at Constant Temperature and Pressure, InternalReportofDivisionofComputerResearchandTechnology,NationalInstitutesofHealth,1988. M.Levitt,MolecularDynamicsofNativeProtein:ComputerSimulationofTrajectories,J.Mol.Biol.,168,595-620(1983) OUT-OF-PLANEDEFORMATIONTERMS J. R. Maple, U. Dinar and A. T. Hagler, Derivation of Force Fields for Molecular Mechanics andDynamicsfromabinitioEnergySurfaces,Proc.Natl.Acad.Sci.USA,85,5350-5354(1988) S.-H.Lee,K.PalmoandS.Krimm,NewOut-of-PlaneAngleandBondAngleInternalCoordinatesandRelatedPotentialEnergyFunctionsforMolecularMechanicsandDynamicsSimulations,J.Comput.Chem.,20,1067-1084(1999) ANALYTICALDERIVATIVESOFPOTENTIALFUNCTIONS K. J. Miller, R. J. Hinde and J. Anderson, First and Second Derivative Matrix Elements for theStretching,Bending,andTorsionalEnergy,J.Comput.Chem.,10,63-76(1989) D.H.FaberandC.Altona,UTAH5:AVersatileProgrammePackagefortheCalculationofMolecularPropertiesbyForceFieldMethods,Computers&Chemistry,1,203-213(1977) W. C. Swope and D. M. Ferguson, Alternative Expressions for Energies and Forces Due to AngleBendingandTorsionalEnergy,ReportG320-3561,J.Comput.Chem.,13,585-594(1992) A.BlondelandM.Karplus,NewFormulationforDerivativesofTorsionAnglesandImproperTorsionAnglesinMolecularMechanics:EliminationofSingularities,J.Comput.Chem.,17,1132-1141(1996) R.E.Tuzun,D.W.NoidandB.G.Sumpter,EfficientTreatmentofOut-of-PlaneBendand ImproperTorsionInteractionsinMM2,MM3,andMM4MolecularMechanicsCalculations, J.Comput.Chem.,18,1804-1811(1997)


TORSIONALSPACEDERIVATIVESANDNORMALMODES M. Levitt, C. Sander and P. S. Stern, Protein Normal-mode Dynamics: Trypsin Inhibitor, Crambin,RibonucleaseandLysozyme,J.Mol.Biol.,181,423-447(1985) M.Levitt,ProteinFoldingbyRestrainedEnergyMinimizationandMolecularDynamics,J.Mol.Biol.,170,723-764(1983) H.WakoandN.Go,AlgorithmforRapidCalculationofHessianofConformationalEnergyFunctionofProteinsbySupercomputer,J.Comput.Chem.,8,625-635(1987) H. Abe, W. Braun, T. Noguti and N. Go, Rapid Calculation of First and Second Derivatives ofConformationalEnergywithRespecttoDihedralAnglesforProteins:GeneralRecurrentEquations,Computers&Chemistry,8,239-247(1984) T.NogutiandN.Go,AMethodofRapidCalculationofaSecondDerivativeMatrixofConformationalEnergyforLargeMolecules,J.Phys.Soc.Japan,52,3685-3690(1983) ANALYTICALSURFACEAREAANDVOLUME M.L.Connolly,AnalyticalMolecularSurfaceCalculation,J.Appl.Cryst.,16,548-558(1983) M.L.Connolly,ComputationofMolecularVolume,J.Am.Chem.Soc.,107,1118-1124(1985) M. L. Connolly, Molecular Surfaces: A Review, available from the web site athttp://www.netsci.org/Science/Compchem/feature14.html C.E.Kundrot, J.W.PonderandF.M.Richards,AlgorithmsforCalculatingExcludedVolumeandItsDerivatives as a Function of Molecular Conformation and Their Use in Energy Minimization, J.Comput.Chem.,12,402-409(1991) T.J.Richmond,SolventAccessibleSurfaceAreaandExcludedVolumeinProteins,J.Mol.Biol.,178,63-89(1984) L.WessonandD.Eisenberg,AtomicSolvationParametersAppliedtoMolecularDynamicsofProteinsinSolution,ProteinScience,1,227-235(1992) V.GononeaandE.Osawa,ImplementationofSolventEffectinMolecularMechanics,Part3.TheFirst-andSecond-orderAnalyticalDerivativesofExcludedVolume,J.Mol.Struct.(Theochem),311305-324(1994) K.D.GibsonandH.A.Scheraga,ExactCalculationof theVolumeandSurfaceAreaofFusedHard-sphereMoleculeswithUnequalAtomicRadii,Mol.Phys.,62,1247-1265(1987) K.D.GibsonandH.A.Scheraga,SurfaceAreaoftheIntersectionofThreeSphereswithUnequalRadii:ASimplifiedAnalyticalFormula,Mol.Phys.,64,641-644(1988) S. Sridharan, A. Nichols and K. A. Sharp, A Rapid Method for Calculating Derivatives of SolventAccessibleSurfaceAreasofMolecules,J.Comput,Chem.,16,1038-1044(1995)


APPROXIMATESURFACEAREAANDVOLUME S. J.Wodakand J. Janin,AnalyticalApproximation to theAccessibleSurfaceAreaofProteins,Proc.Natl.Acad.Sci.USA,77,1736-1740(1980) W.Hasel,T.F.HendricksonandW.C.Still,ARapidApproximationtotheSolventAccessibleSurfaceAreasofAtoms,TetrahedronComput.Method.,1,103-116(1988) J. Weiser, P. S. Shenkin and W. C. Still, Approximate Solvent-Accessible Surface Areas fromTetrahedrallyDirectedNeighberDensities,Biopolymers,50,373-380(1999) BOUNDARYCONDITIONSANDNEIGHBORMETHODS W.F.vanGunsteren,H. J.C.Berendsen,F.Colonna,D.Perahia, J.P.HollenbergandD.Lellouch,OnSearchingNeighborsinComputerSimulationsofMacromolecularSystems,J.Comput.Chem.,5,272-279(1984) F. Sullivan, R.D.Mountainand J. O'Connell,MolecularDynamics onVector Computers, J. Comput.Phys.,61,138-153(1985) J. Boris, A Vectorized ``Near Neighbors'' Algorithm of Order N Using aMonotonic Logical Grid, J.Comput.Phys.,66,1-20(1986) S.G.LambrakosandJ.P.Boris,GeometricPropertiesoftheMonotonicLagrangianGridAlgorithmforNearNeighborsCalculations,J.Comput.Phys.,73,183-202(1987) T.A.Andrea,W.C.SwopeandH.C.Andersen,TheRoleofLongRangedForcesinDeterminingtheStructureandPropertiesofLiquidWater,J.Chem.Phys.,79,4576-4584(1983) D. N. Theodorou and U. W. Suter, Geometrical Considerations in Model Systems with PeriodicBoundaryConditions,J.Chem.Phys.,82,955-966(1985) J. Barnes and P. Hut, A Hierarchical O(NlogN) Force-calculation Algorithm,Nature, 234, 446-449(1986) CUTOFFANDTRUNCATIONMETHODS P. J. Steinbach and B. R. Brooks, New Spherical-Cutoff Methods for Long-Range Forces inMacromolecularSimulation,J.Comput.Chem.,15,667-683(1993) R.J.LoncharichandB.R.Brooks,TheEffectsofTruncatingLong-RangeForcesonProteinDynamics,Proteins,6,32-45(1989) C. L. Brooks III, B.M. Pettitt andM. Karplus, Structural and Energetic Effects of Truncating LongRangedInteractionsinIonicandPolarFluids,J.Chem.Phys.,83,5897-5908(1985) EWALDSUMMATIONTECHNIQUES A. Y. Toukmaji and J. A. Board, Jr., Ewald SummationTechniques in Perspective: A Survey,Comp.Phys.Commun.,95,73-92(1996)


T.Darden,L.Perera,L.LiandL.Pedersen,NewTricksforModelersfromtheCrystallographyToolkit:TheParticleMeshEwaldAlgorithmanditsUseinNucleicAcidSimulations,Structure,7,R550-R60(1999) T.Darden,D.YorkandL.G.Pedersen,ParticleMeshEwald:AnN∑log(N)MethodforEwaldSumsinLargeSystems,J.Chem.Phys.,98,10089-10092(1993) U.Essmann,L.Perera,M.L.Berkowitz,T.Darden,H.LeeandL.G.Pedersen,ASmoothParticleMeshEwaldMethod,J.Chem.Phys.,103,8577-8593(1995) W.Smith,PointMultipolesintheEwaldSummation(Revisited),CCP5Newsletter,46,18-30(1998)[availablefromhttp://www.dl.ac.uk/CCP/CCP5/newsletter_index.html] S. E. Feller, R.W. Pastor, A. Rojnuckarin, S. Bogusz and B. R. Brooks, Effect of Electrostatic ForceTruncation on Interfacial and Transport Properties of Water, J. Phys. Chem., 100, 17011-17020(1996) W.Weber,P.H.H¸nenbergerandJ.A.McCammon,MolecularDynamicsSimulationsofaPolyalanineOctapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on PeptideConformation,J.Phys.Chem.B,104,3668-3675(2000) CONJUGATEDANDAROMATICSYSTEMS N. L. Allinger, F. Li, L. Yan and J. C. Tai, Molecular Mechanics (MM3) Calculations on ConjugatedHydrocarbons,J.Comput.Chem.,11,868-895(1990) J.T.Sprague,J.C.Tai,Y.YuhandN.L.Allinger,TheMMP2CalculationalMethod,J.Comput.Chem.,8,581-603(1987) J.Kao,AMolecularOrbitalBasedMolecularMechanicsApproachtoStudyConjugatedHydrocarbons,J.Am.Chem.Soc.,109,3818-3829(1987) J.KaoandN.L.Allinger,ConformationalAnalysis:HeatsofFormationofConjugatedHydrocarbonsbytheForceFieldMethod,J.Am.Chem.Soc.,99,975-986(1977) D.H.LoandM.A.Whitehead,AccurateHeatsofAtomizationandAccurateBondLengths:BenzenoidHydrocarbons,Can.J.Chem.,46,2027-2040(1968) G. D. Zeiss and M. A. Whitehead, Hetero-atomic Molecules: Semi-empirical Molecular OrbitalCalculationsandPredictionofPhysicalProperties,J.Chem.Soc.A,1727-1738(1971) FREEENERGYSIMULATIONMETHODS P.Kollman,FreeEnergyCalculations:ApplicationstoChemicalandBiochemicalPhenomena,Chem.Rev.,93,2395-2417(1993) B.L.TembeandJ.A.McCammon,Ligand-ReceptorInteractions,Computers&Chemistry,8,281-283(1984)


W. L. Jorgensen and C. Ravimohan, Monte Carlo Simulation of Differences in Free Energy ofHydration,J.Chem.Phys.,83,3050-3054(1985) W.L.Jorgensen,J.K.Buckner,S.BoudonandJ.Tirado-Rives,EfficientComputationofAbsoluteFreeEnergiesofBindingbyComputerSimulations:ApplicationtotheMethaneDimerinWater,J.Chem.Phys.,89,3742-3746(1988) S.H.FleischmanandC.L.BrooksIII,ThermodynamicsofAqueousSolvation:SolutionPropertiesofAlcoholsandAlkanes,J.Chem.Phys.,87,3029-3037(1987) U.C.Singh,F.K.Brown,P.A.BashandP.A.Kollman,AnApproachtotheApplicationofFreeEnergyPerturbationMethodsUsingMolecularDynamics,J.Am.Chem.Soc.,109,1607-1614(1987) D. A. Pearlman and P. A. Kollman, A New Method for Carrying out Free Energy PerturbationCalculations:DynamicallyModifiedWindows,J.Chem.Phys.,90,2460-2470(1989) T. P. Straatsma,H. J.C. Berendsen and J. P.M.Postma,FreeEnergy ofHydrophobicHydration: AMolecularDynamicsStudyofNobleGasesinWater,J.Chem.Phys.,85,6720-6727(1986) T.P.StraatsmaandH.J.C.Berendsen,FreeEnergyofIonicHydration:AnalysisofaThermodynamicIntegration Technique to Evaluate Free EnergyDifferences byMolecular Dynamics Simulations, J.Chem.Phys.,89,5876-5886(1988) M.Mezei, The Finite Difference Thermodynamic Integration, Tested on Calculating the HydrationFreeEnergyDifferencebetweenAcetoneandDimethylamineinWater,J.Chem.Phys.,86,7084-7088(1987) A. E. Mark andW. F. van Gunsteren, Decomposition of the Free Energy of a System in Terms ofSpecificInteractions,J.Mol.Biol.,240,167-176(1994) S.BoreschandM.Karplus,TheMeaningofCopmponentAnalysis:DecompositionoftheFreeEnergyinTermsofSpecificInteractions,J.Mol.Biol.,254,801-807(1995) METHODSFORPARAMETERDETERMINATION N.L.Allinger,X.ZhouandJ.Bergsma,MolecularMechanicsParameters,J.Mol.Struct.(THEOCHEM),312,69-83(1994) A. J. Pertsin andA. I. Kitaigorodsky,TheAtom-AtomPotentialMethod:Application toOrganicMolecularSolids,Springer-Verlag,Berlin,1987 D. E. Williams, Transferable Empirical Nonbonded Potential Functions, in Crystal Cohesion andConformationalEnergies,Ed.byR.M.Metzger,Springer-Verlag,Berlin,1981 A.T.HaglerandS.Lifson,AProcedureforObtainingEnergyParametersfromCrystalPacking,ActaCryst.,B30,1336-1341(1974) A. T. Hagler, S. Lifson and P. Dauber, Consistent Force Field Studies of Intermolecular Forces inHydrogen-BondedCrystals:ABenchmarkfortheObjectiveComparisonofAlternativeForceFields,J.Am.Chem.Soc.,101,5122-5130(1979)


W.L. Jorgensen, J.D.Madura andC. J. Swenson,Optimized Intermolecular Potential Functions forLiquidHydrocarbons,J.Am.Chem.Soc.,106,6638-6646(1984) W. L. Jorgensen and C. J. Swenson, Optimized Intermolecular Potential Functions for Amides andPeptides:StructureandPropertiesofLiquidAmides,J.Am.Chem.Soc.,107,569-578(1985) J. R. Maple, U. Dinur and A. T. Hagler, Derivation of Force Fields for Molecular Mechanics andDynamicsfromabInitioSurfaces,Proc.Nat.Acad.Sci.USA,85,5350-5354(1988) U.DinurandA.T.Hagler,DirectEvaluationofNonbondingInteractionsfromabInitioCalculations,J.Am.Chem.Soc.,111,5149-5151(1989) ELECTROSTATICINTERACTIONS S. L. Price, Towards More Accurate Model Intermolecular Potentials for Organic Molecules, Rev.Comput.Chem.,14,225-289(2000) C. H. Faerman and S. L. Price, A Transferable Distributed Multipole Model for the ElectrostaticInteractionsofPeptidesandAmides,J.Am.Chem.Soc.,112,4915-4926(1990) C. E.Dykstra, Electrostatic InteractionPotentials inMolecular Force Fields,Chem.Rev.,93, 2339-2353(1993) M. J. Dudek and J. W. Ponder, Accurate Modeling of the Intramolecular Electrostatic Energy ofProteins,J.Comput.Chem.,16,791-816(1995) U.KochandE.Egert,AnImprovedDescriptionoftheMolecularChargeDensityinForceFieldswithAtomicMultipoleMoments,J.Comput.Chem.,16,937-944(1995) D.E.Williams,RepresentationoftheMolecularElectrostaticPotentialbyAtomicMultipoleandBondDipoleModels,J.Comput.Chem.,9,745-763(1988) F. Colonna, E. Evleth and J. G. Angyan, Critical Analysis of Electric Field Modeling: Formamide, J.Comput.Chem.,13,1234-1245(1992) POLARIZATIONEFFECTS S. Kuwajima and A. Warshel, Incorporating Electric Polarizabilities in Water-Water InteractionPotentials,J.Phys.Chem.,94,460-466(1990) J. W. Caldwell and P. A. Kollman, Structure and Properties of Neat Liquids Using NonadditiveMolecular Dynamics: Water, Methanol, and N-Methylacetamide, J. Phys. Chem., 99, 6208-6219(1995) D.N.Bernardo,Y.Ding,K.Kroegh-JespersenandR.M.Levy,AnAnisotropicPolarizableWaterModel:IncorporationofAll-AtomPolarizabilitiesintoMolecularMechanicsForceFields,J.Phys.Chem.,98,4180-4187(1994)


P. T. van Duijnen andM. Swart,Molecular and Atomic Polarizabilities: Thole'sModel Revisited, J.Phys.Chem.A,102,2399-2407(1998) K. J. Miller, Calculation of theMolecular Polarizability Tensor, J. Am. Chem. Soc., 112, 8543-8551(1990) J.Applequist,J.R.CarlandK.-K.Fung,AnAtomDipoleInteractionModelforMolecularPolarizability.ApplicationtoPolyatomicMoleculesandDeterminationofAtomPolarizabilities,J.Am.Chem.Soc.,94,2952-2960(1972) J.Applequist,AtomChargeTransferinMolecularPolarizabilities.ApplicationoftheOlson-SundbergModeltoAliphaticandAromaticHydrocarbons,J.Phys.Chem.,97,6016-6023(1993) A.J.Stone,DistributedPolarizabilities,Mol.Phys.,56,1065-1082(1985) J.M.StoutandC.E.Dykstra,ADistributedModeloftheElectricalResponseofOrganicMolecules,J.Phys.Chem.A,102,1576-1582(1998) MACROSCOPICTREATMENTOFSOLVENT C. J. Cramer and D. G. Truhlar, Continuum Solvation Models: Classical and Quantum MechanicalImplementations,Rev.Comput.Chem.,6,1-72(1995) B.RouxandT.Simonson,ImplicitSolvationModels,Biophys.Chem.,78,1-20(1999) M.K. Gilson, Introduction toContinuumElectrostaticswithMolecularApplications,available fromhttp://gilsonlab.umbi.umd.edu SURFACEAREA-BASEDSOLVATIONMODELS D.EisenbergandA.D.McLachlan,SolvationEnergyinProteinFoldingandBinding,Nature,319,199-203(1986) L.WessonandD.Eisenberg,AtomicSolvationParametersAppliedtoMolecularDynamicsofProteinsinSolution,Prot.Sci.,1,227-235(1992) T.Ooi,M.Oobatake,G.NemethyandH.A.Scheraga, Accessible SurfaceAreasasaMeasure of theThermodynamic Parameters of Hydration of Peptides,Proc. Natl. Acad. Sci. USA, 84, 3086-3090(1987) J.D.AugspurgerandH.A.Scheraga,AnEfficient,DifferentiableHydrationPotentialforPeptidesandProteins,J.Comput.Chem.,17,1549-1558(1996) GENERALIZEDBORNSOLVATIONMODELS W.C.Still,A.Tempczyk,R.C.HawleyandT.Hendrickson,ASemiempiricalTreatmentofSolvationforMolecularMechanicsandDynamics,J.Am.Chem.Soc.,112,6127-6129(1990)


D.Qiu,P.S.Shenkin,F.P.HollingerandW.C.Still,TheGB/SAContinuumModelforSolvation.AFastAnalyticalMethodfortheCalculationofApproximateBornRadii,J.Phys.Chem.A,101,3005-3014(1997) G.D.Hawkins,C.J.CramerandD.G.Truhlar,PairwiseSoluteDescreeningofSoluteChargesfromaDielectricMedium,Chem.Phys.Lett.,246,122-129(1995) G. D. Hawkins, C. J. Cramer and D. G. Truhlar, ParametrizedModels of Aqueous Free Energies ofSolvationBasedonPairwiseDescreeningofSoluteAtomicChargesfromaDielectricMedium,J.Phys.Chem.,100,19824-19839(1996) A. Onufriev, D. Bashford and D. A. Case, Modification of the Generalized Born Model Suitable forMacromolecules,J.Phys.Chem.B,104,3712-3720(2000) M.SchaeferandM.Karplus,AComprehensiveAnalyticalTreatmentofContinuumElectrostatics, J.Phys.Chem.,100,1578-1599(1996) M.Schaefer,C.BartelsandM.Karplus,SolutionConformationsandThermodynamicsofStructuredPeptides:MolecularDynamicsSimulationwithanImplicitSolvationModel,J.Mol.Biol.,284,835-848(1998) SUPERPOSITIONOFCOORDINATESETS S. J. Kearsley, An Algorithm for the Simultaneous Superposition of a Structural Series, J. Comput.Chem.,11,1187-1192(1990) R.Diamond,ANoteontheRotationalSuperpositionProblem,ActaCryst.,A44,211-216(1988) A.D.McLachlan,RapidComparisonofProteinStructures,ActaCryst.,A38,871-873(1982) S.C.Nyburg,SomeUsesofaBestMolecularFitRoutine,ActaCryst.,B30,251-253(1974) LOCATIONOFTRANSITIONSTATES R.CzerminskiandR.Elber,ReactionPathStudyofConformationalTransitionsandHelixFormationinaTetrapeptide,Proc.Nat.Acad.Sci.USA,86,6963(1989) R.S.Berry,H.L.DavisandT.L.Beck,FindingSaddlesonMultidimensionalPotentialSurfaces,Chem.Phys.Lett.,147,13(1988) K.Muller,ReactionPathsonMultidimensionalEnergyHypersurfaces,Ang.Chem.Int.Ed.Engl.,19,1-13(1980) S.BellandJ.S.Crighton,LocatingTransitionStates,J.Chem.Phys.,80,2464-2475(1984) S.FischerandM.Karplus,ConjugatePeakRefinement:AnAlgorithmforFindingReactionPathsandAccurateTransitionStatesinSystemswithManyDegreesofFreedom,Chem.Phys.Lett.,194,252-261(1992)


J. E.SinclairandR.Fletcher, ANewMethod of Saddle-Point Location for theCalculation ofDefectMigrationEnergies,J.Phys.C,7,864-870(1974) R.ElberandM.Karplus,AMethodforDeterminingReactionPathsinLargeMolecules:ApplicationtoMyoglobin,Chem.Phys.Lett.,139,375-380(1987) D. T. Nguyen and D. A. Case, On Finding Stationary States on Large-Molecule Potential EnergySurfaces,J.Phys.Chem.,89,4020-4026(1985) T. A. Halgren and W. N. Lipscomb, The Synchronous-Transit Method for Determining ReactionPathwaysandLocatingMolecularTransitionStates,Chem.Phys.Lett.,49,225-232(1977) G.T.BarkemaandN.Mousseau, Event-BasedRelaxation of ContinuousDisordered Systems,Phys.Rev.Lett.,77,4358-4361(1996)

version .0 2fwrehu 20 software tools for - jay ponder lab

Documents