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1、Chapter4ComparisonofProteinForceFieldsforMolecularDynamicsSimulationsOlgunGuvenchandAlexanderD.MacKerell,Jr.SummaryInthecontextofmoleculardynamicssimulationsofproteins,thetermÒforceÞeldÓreferstothecombinationofamathematicalformulaandassoci-atedparametersth
2、atareusedtodescribetheenergyoftheproteinasafunctionofitsatomiccoordinates.Inthisreview,wedescribethefunctionalformsandparameterizationprotocolsofthewidelyusedbiomolecularforceÞeldsAmber,CHARMM,GROMOS,andOPLS-AA.Wealsosummarizetheabilityofvariousreadilyavai
3、lablenoncommercialmoleculardynamicspackagestoperformsimula-tionsusingtheseforceÞelds,aswellastousemodernmethodsforthegenerationofconstant-temperature,constant-pressureensemblesandtotreatlong-rangeinter-actions.Finally,weÞnishwithadiscussionoftheabilityofth
4、eseforceÞeldstosupportthemodelingofproteinsinconjunctionwithnucleicacids,lipids,carbohy-drates,and/orsmallmolecules.Keywords:Amber·CHARMM·GROMOS·Moleculardynamics·OPLS-AA·Protein1IntroductionClassicalmoleculardynamics(MD)simulationsofproteinsarefoundedonth
5、eideaofusingadifferentiablefunctionoftheatomiccoordinatestorepresenttheenergyofthesystem.Thisfunctionisanapproximationofthetruequantummechanical(QM)wavefunction.ThefunctionÕspartialderivativeswithrespecttotheatomicCartesiancoordinatesyieldforcesthatcanthen
6、beusedtopropagatethesystemthroughtimeusingclassicalmechanics.Inadditiontobeingdependentontheatomiccoordinates,thefunctionÕsvaluealsodependsonasetofparametersthatdescribethegeometricandenergeticpropertiesofinterparticleinteractions.Unlikethecoordinates,thes
7、eparametersareinvariantduringthecourseofasimulation.ThecombinationofthemathematicalfunctionandtheparametersiscommonlyreferredtoasaÒforceÞeld.ÓFrom:MethodsinMolecularBiology,vol.443,MolecularModelingofProteinsEditedbyAndreasKukolcHumanaPress,Totowa,NJ6364O
8、.Guvench,A.D.MacKerell,Jr.Inthisreview,wewillfocusonthewidelyusedbiomolecularproteinforceÞeldsAmber[1],CHARMM[2],GROMOS[3],andOPLS-AA[4],whichaccountforthemajorityofrecentlypublishedMDsimulationsofproteins.Al
