MacroModel Reference Manual - ISP

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Appendix D: Force-Field File Format2 MM2 asymmetric stretch3 MM3 symmetric stretchBend0 None1 Symmetric (Hooke’s law) bend2 MM2 asymmetric bend3 MM3 asymmetric bend4 MMFF asymmetric bendStretch-Bend0 None1 Linear, one constant for both bonds (MM2, MM3)2 Linear, separate constants for each bone (MMFF)Torsion0 None1 MM2-style cosine torsional potential2 AMBER-style cosine torsional potential3 OPLS-style cosine torsional potential with explicit V0Improper Torsion (Out-of-Plane)0 None1 Harmonic out-of-plane (MM2)2 Improper torsion3 Improper torsion with explicit V04 Harmonic Wilson-angle displacement (MMFF)192MacroModel 9.7 Reference Manual
Appendix D: Force-Field File FormatVan der Waals1 7,11-Lennard-Jones equation; Eps, R as defined in AMBER2 6,12-Lennard Jones Equation; Eps, R as defined in AMBER3 MM3 Hill Equation; Eps, R4 MM2 Hill Equation; Eps, R5 Lennard Jones Equation; Eps, R as defined in OPLS6 Lennard Jones Equation; Alpha, R, N as defined in CHARMM7 MMFF buffered 7,14 potentialCoulombic0 Turned off1 Constant-dielectric electrostatics2 Distance-dependent (R) dielectric electrostatics3 MMFF buffered constant dielectric constant4 MMFF buffered, distance-dependent dielectric constantHydrogen-bonding0 6,12-Lennard Jones for hydrogen bonds1 10,12-Lennard Jones hydrogen bonds2 10,12 Lennard-Jones with angular dependenceSpecial Treatment of 1–4 Interactions0 Skip all 1,4 electrostatics and van der Waals1 Scale 1,4 van der Waals terms by factor given2 Scale 1,4 Coulombic terms by factor given3 Scale both 1,4 van der Waals and electrostatics by factor given4 Do not scale 1,4 nonbonded interactionsMacroModel 9.7 Reference Manual 193
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MacroModel Reference ManualMacroMod
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ContentsDocument Conventions ......
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ContentsChapter 5: MINTA...........
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Document ConventionsIn addition to
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MacroModel Reference ManualChapter
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Chapter 1: Capabilities and New Fea
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Chapter 2: Running MacroModelTable
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Chapter 2: Running MacroModelstruct
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Chapter 2: Running MacroModel2.2 Jo
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Chapter 2: Running MacroModelfile
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Chapter 2: Running MacroModelusing
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Chapter 2: Running MacroModel2.3.3.
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Chapter 2: Running MacroModelalso s
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Chapter 3: Running MacroModel with
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Chapter 4: Operation Codesarg1Frequ
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Chapter 4: Operation Codesarg3Hydro
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Chapter 4: Operation CodesTable 4.1
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Chapter 4: Operation CodesLimitatio
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Chapter 4: Operation Codesarg3Note:
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Chapter 4: Operation Codes2 Use for
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Chapter 4: Operation Codes1 The cur
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Chapter 4: Operation Codes1 Use fas
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Chapter 4: Operation Codesway on th
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Chapter 4: Operation Codes
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Chapter 4: Operation CodesIf solvat
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Chapter 4: Operation CodesFMNR has
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Chapter 4: Operation Codesarg1Listi
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Chapter 4: Operation Codesnarg3For
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Chapter 4: Operation Codesarg3 Symm
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Chapter 4: Operation Codes4.7 Const
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Chapter 4: Operation CodesIf a SUBS
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Chapter 4: Operation CodesASL3 —
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Chapter 4: Operation Codes>0 Specif
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Chapter 4: Operation CodesThe const
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Chapter 4: Operation Codesarg2Clear
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Chapter 4: Operation CodesADDC —
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Chapter 4: Operation Codesarg7Compa
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Chapter 4: Operation CodesFor examp
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Chapter 4: Operation Codesarg1arg2a
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Chapter 4: Operation Codes4 Rotate
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Chapter 4: Operation Codesarg1−1A
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Chapter 4: Operation CodesAUOP —
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Chapter 4: Operation CodesLMCS can
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Chapter 4: Operation CodesLMC2 is i
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Chapter 4: Operation Codesarg6Allow
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Chapter 4: Operation Codes• Rings
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Chapter 4: Operation Codesarg1Param
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Chapter 4: Operation Codes2 H×v is
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Chapter 4: Operation Codesarg8Spars
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Chapter 4: Operation CodesSPMC sear
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Chapter 4: Operation Codes0 Use set
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Chapter 4: Operation Codes−1arg5D
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Chapter 4: Operation Codesarg2 Line
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Chapter 4: Operation CodesSEED —
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Chapter 4: Operation Codesfrom with
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Chapter 4: Operation Codesarg1-4Ato
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Chapter 4: Operation CodesnWrite ev
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Chapter 4: Operation Codesarg3Molec
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Chapter 4: Operation Codes0 Time in
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Chapter 4: Operation CodesMDAP —
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Chapter 4: Operation CodesMHBD —
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Chapter 4: Operation CodesMDFT —
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Chapter 4: Operation Codesment. We
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Chapter 4: Operation Codesarg7Time_
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Chapter 4: Operation Codesarg6Inter
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Chapter 4: Operation Codes1 Do not
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Chapter 4: Operation Codesarg 8Maxi
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Chapter 4: Operation CodesThis comm
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Page 177 and 178: Chapter 5: MINTAature. Note that H
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Page 183 and 184: Chapter 5: MINTAtion (25,000 total
Page 185 and 186: MacroModel Reference ManualAppendix
Page 191 and 192: Appendix C: Atom and Bond TypesTabl
Page 199: Appendix D: Force-Field File Format
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Page 231 and 232: Appendix E: The BMFF ProtocolBefore
Page 237 and 238: Appendix G: MINTA BackgroundL(s)
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Page 241 and 242: Appendix G: MINTA BackgroundDirect
Page 243 and 244: Appendix G: MINTA BackgroundPaulsen
Page 245 and 246: MacroModel Reference ManualReferenc
Page 247 and 248: References26. Sefler, A. M.; Lauri,
Page 249 and 250: References52. Kaminski, G. A.; Frie
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Opcode IndexBold face page numbers
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Opcode IndexRRHO...................
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