MacroModel Reference Manual - ISP

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Appendix C: Atom and Bond TypesTable C.1. Bond order values and symbols.Value Symbol Description0 . Zero order bond1 - Single bond2 = Double bond3 % Triple bond4 * Bond of undefined order (excluding zero order)C.3 MacroModel Atom TypesThe following table lists the atom types that are used in MacroModel and their equivalencies toatom types for other force fields. These atom types are defined in the atom.typ file. SeeSection C.1 on page 181 for a description of the atom.typ file and how to add atom types.Note that in MacroModel, 00 atoms are stored as type 0 in the atom connection table, and thatall current force fields require explicit hydrogens on heteroatoms.Table C.2. Atom types and equivalents.EquivalenciesNo. Symbol DescriptionMM2/MM3 Charmm Amber1 C1 Carbon - sp2 C2 Carbon - sp 2 2,3 CT,C C, C*, CA,CB, CC, CM,CF, CG, CN3 C3 Carbon - sp 3 1 CT CT4 CA United atom CH - sp 3 CH1E CH5 CB United atom CH 2 - sp 3 CH2E C26 CC United atom CH 3 - sp 3 CH3E C37 CD United atom CH - sp 2 CR1E CD, CE, CJ,CP8 CE United atom CH 2 - sp 29 CF United atom CH - sp10 CM Carbanion (C – )182MacroModel 9.7 Reference Manual
Appendix C: Atom and Bond TypesTable C.2. Atom types and equivalents. (Continued)EquivalenciesNo. Symbol DescriptionMM2/MM3 Charmm Amber11 CP Carbocation (C + ) 3012 CR Carbon free radical 29...14 C0 Any carbon15 O2 Oxygen - double bond 7 O O, O216 O3 Oxygen - single bond 6 OH1, OH2 OS, OH17 OA United atom OH OH1E18 OM O − (alkoxide, carboxylate) 47 OC19 OW United atom H 2 O OH2E20 OP Oxonium (sp 2 ) =[O + ]–21 OQ Oxonium (sp 3 ) R 3 O +...23 O0 Any oxygen24 N1 Nitrogen - sp 1025 N2 Nitrogen - sp 2 9 N, NR, NP,NH1, NH226 N3 Nitrogen - sp 3 8 NH3 NT27 NA United atom NH - sp 328 NB United atom NH 2 - sp 3 NH1E29 NC United atom NH - sp 230 ND United atom NH 2 - sp 2 NH2E31 N4 N + - sp 2 NC2 NA32 N5 N + - sp 3 39 N333 NE United atom NH + - sp 334 NF United atom NH 2 + - sp 335 NG United atom NH 3 + - sp 3 NH3EN, NB, NC,N*, N2MacroModel 9.7 Reference Manual 183
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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 Codes2 Use for
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Chapter 4: Operation Codes1 The cur
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Chapter 4: Operation Codesment. We
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Page 185 and 186: MacroModel Reference ManualAppendix
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Page 193 and 194: Appendix C: Atom and Bond TypesTabl
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Page 199 and 200: Appendix D: Force-Field File Format
Page 231 and 232: Appendix E: The BMFF ProtocolBefore
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Appendix G: MINTA BackgroundDirect
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Appendix G: MINTA BackgroundPaulsen
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MacroModel Reference ManualReferenc
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References26. Sefler, A. M.; Lauri,
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References52. Kaminski, G. A.; Frie
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Opcode IndexBold face page numbers
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Opcode IndexRRHO...................
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