MacroModel Reference Manual - ISP

More documents

Recommendations

Info

Appendix D: Force-Field File FormatC Benzenoids (Beckhaus, ChemBer, 116, 86 (1983))9 C2*C2*AA*AA*AA*AA*1-21 1 2 1.3900 8.0667 0.00002 1 2 3 120.0000 0.43004 00 1 2 00 0.0000 36.8000 0.0000The usual torsional parameter handling in substructures is that all parameters (V 1 ,V 2 , and V 3 )for a matched torsional interaction are overwritten by the torsional parameters from a torsionalsubstructure parameter line. It is possible to overwrite only specific components (e.g., only theV 2 component) by using the special parameter entry 99.9999 for the other components; thisprevents overwriting. For example, the torsional parameter line below would replace only theV 2 barrier (with 2.5 kcal/mol) of an existing torsional interaction.4 00 2 3 00 99.9999 2.5000 99.9999Note again that the V 2 barrier specified here is the total barrier, because of the use of wild-cardatom types.Figure D.10 on page 217 shows how a specific set of charges (perhaps derived from ab initioquantum-mechanical studies) can be specified directly in a substructure. The purpose of thesubstructure above is to load the partial charges given in the line beginning 8. The charges areplaced on the substructure atoms in the order in which the atoms appear in the substructurenotation. When using partial charges directly instead of bond dipoles, be sure that the totalcharge of the substructure sums to 0.0 for neutral substructures. Also check the final charge setusing Maestro (the Electrostatics panel) to test your charge data.D.4.5Geometry-dependent ParametersIt is occasionally desirable to make the parameters used for certain degrees of freedom dependentupon the geometry of some other degree of freedom. We allow this, in a limited sense.First, the degree of freedom which dictates the parameters must be configurational; that is, wedo not provide a mechanism for “on-the-fly” reparameterization of atoms, but only for parameterizingsome degree of freedom based on the initial value of some other. Second, we providethree specific forms of this dependence. First of all, a parameter for an interaction can dependon a torsion value, and secondly a parameter for an interaction can depend on whether theinteraction is within a ring; finally, a parameter can depend on the initial value of an angle. Thefollowing examples illustrate several cases.216MacroModel 9.7 Reference Manual
Appendix D: Force-Field File FormatFigure D.10.-3C Imidazolium (AMBER HIP)9 CU-N4=CU-N2-CU=1-21 1 2 1.3830 424.5000...8 0.1160 0.2480 0.2720 0.2480 0.1160 O 1 1 a JCC, 230 (86)8 0.3530 -0.2125 0.7190 -0.2125 0.3530 O 1 1 b JACS, 765 (84)MacroModel 9.7 Reference Manual 217
Page 1 and 2:
MacroModel Reference ManualMacroMod
Page 3 and 4:
ContentsDocument Conventions ......
Page 5 and 6:
ContentsChapter 5: MINTA...........
Page 7 and 8:
Document ConventionsIn addition to
Page 9 and 10:
MacroModel Reference ManualChapter
Page 11 and 12:
Chapter 1: Capabilities and New Fea
Page 13 and 14:
Page 15 and 16:
Page 17 and 18:
Page 19 and 20:
Page 21 and 22:
Chapter 2: Running MacroModelTable
Page 23 and 24:
Chapter 2: Running MacroModelstruct
Page 25 and 26:
Chapter 2: Running MacroModel2.2 Jo
Page 27 and 28:
Chapter 2: Running MacroModelfile
Page 29 and 30:
Chapter 2: Running MacroModelusing
Page 31 and 32:
Chapter 2: Running MacroModel2.3.3.
Page 33 and 34:
Chapter 2: Running MacroModelalso s
Page 35 and 36:
Page 37 and 38:
Chapter 3: Running MacroModel with
Page 39 and 40:
Page 41 and 42:
Chapter 4: Operation Codesarg1Frequ
Page 43 and 44:
Chapter 4: Operation Codesarg3Hydro
Page 45 and 46:
Chapter 4: Operation CodesTable 4.1
Page 47 and 48:
Chapter 4: Operation CodesLimitatio
Page 49 and 50:
Chapter 4: Operation Codesarg3Note:
Page 51 and 52:
Chapter 4: Operation Codes2 Use for
Page 53 and 54:
Chapter 4: Operation Codes1 The cur
Page 55 and 56:
Chapter 4: Operation Codes1 Use fas
Page 57 and 58:
Chapter 4: Operation Codesway on th
Page 59 and 60:
Chapter 4: Operation Codes
Page 61 and 62:
Chapter 4: Operation CodesIf solvat
Page 63 and 64:
Chapter 4: Operation CodesFMNR has
Page 65 and 66:
Chapter 4: Operation Codesarg1Listi
Page 67 and 68:
Chapter 4: Operation Codesnarg3For
Page 69 and 70:
Chapter 4: Operation Codesarg3 Symm
Page 71 and 72:
Chapter 4: Operation Codes4.7 Const
Page 73 and 74:
Chapter 4: Operation CodesIf a SUBS
Page 75 and 76:
Chapter 4: Operation CodesASL3 —
Page 77 and 78:
Chapter 4: Operation Codes>0 Specif
Page 79 and 80:
Chapter 4: Operation CodesThe const
Page 81 and 82:
Chapter 4: Operation Codesarg2Clear
Page 83 and 84:
Chapter 4: Operation CodesADDC —
Page 85 and 86:
Chapter 4: Operation Codesarg7Compa
Page 87 and 88:
Chapter 4: Operation CodesFor examp
Page 89 and 90:
Chapter 4: Operation Codesarg1arg2a
Page 91 and 92:
Chapter 4: Operation Codes4 Rotate
Page 93 and 94:
Chapter 4: Operation Codesarg1−1A
Page 95 and 96:
Chapter 4: Operation CodesAUOP —
Page 97 and 98:
Chapter 4: Operation CodesLMCS can
Page 99 and 100:
Chapter 4: Operation CodesLMC2 is i
Page 101 and 102:
Chapter 4: Operation Codesarg6Allow
Page 103 and 104:
Chapter 4: Operation Codes• Rings
Page 105 and 106:
Chapter 4: Operation Codesarg1Param
Page 107 and 108:
Chapter 4: Operation Codes2 H×v is
Page 109 and 110:
Chapter 4: Operation Codesarg8Spars
Page 111 and 112:
Chapter 4: Operation CodesSPMC sear
Page 113 and 114:
Chapter 4: Operation Codes0 Use set
Page 115 and 116:
Chapter 4: Operation Codes−1arg5D
Page 117 and 118:
Chapter 4: Operation Codesarg2 Line
Page 119 and 120:
Chapter 4: Operation CodesSEED —
Page 121 and 122:
Chapter 4: Operation Codesfrom with
Page 123 and 124:
Chapter 4: Operation Codesarg1-4Ato
Page 125 and 126:
Chapter 4: Operation CodesnWrite ev
Page 127 and 128:
Chapter 4: Operation Codesarg3Molec
Page 129 and 130:
Chapter 4: Operation Codes0 Time in
Page 131 and 132:
Chapter 4: Operation CodesMDAP —
Page 133 and 134:
Chapter 4: Operation CodesMHBD —
Page 135 and 136:
Chapter 4: Operation CodesMDFT —
Page 137 and 138:
Chapter 4: Operation Codesment. We
Page 139 and 140:
Chapter 4: Operation Codesarg7Time_
Page 141 and 142:
Chapter 4: Operation Codesarg6Inter
Page 143 and 144:
Chapter 4: Operation Codes1 Do not
Page 145 and 146:
Chapter 4: Operation Codesarg 8Maxi
Page 147 and 148:
Chapter 4: Operation CodesThis comm
Page 149 and 150:
Chapter 4: Operation Codes4.15 Misc
Page 151 and 152:
Chapter 4: Operation Codes45 [NEW]
Page 153 and 154:
Chapter 4: Operation Codes100 Set n
Page 155 and 156:
Chapter 4: Operation Codes252 GV, c
Page 157 and 158:
Chapter 4: Operation Codes931 Turns
Page 159 and 160:
Chapter 4: Operation Codesarg2arg3a
Page 161 and 162:
Chapter 4: Operation Codesarg1Numbe
Page 163 and 164:
Chapter 4: Operation Codes4.16 Conf
Page 165 and 166:
Chapter 4: Operation Codes−3do no
Page 167 and 168:
Chapter 4: Operation Codesarg7Minim
Page 169 and 170:
Chapter 4: Operation CodesConfGen i
Page 171 and 172:
Chapter 4: Operation Codesarg6Maxim
Page 173 and 174: MacroModel Reference ManualChapter
Page 175 and 176: Chapter 5: MINTAthat energy well. N
Page 177 and 178: Chapter 5: MINTAature. Note that H
Page 179 and 180: Chapter 5: MINTA0 Numerical integra
Page 181 and 182: Chapter 5: MINTAconformational sear
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 and 200: Appendix D: Force-Field File Format
Page 223: Appendix D: Force-Field File Format
Page 231 and 232: Appendix E: The BMFF ProtocolBefore
Page 237 and 238: Appendix G: MINTA BackgroundL(s)
Page 239 and 240: Appendix G: MINTA Backgroundpath in
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
Page 251 and 252: Opcode IndexBold face page numbers
Page 253 and 254: Opcode IndexRRHO...................
Page 256: 120 West 45th Street, 29th FloorNew
show all

MacroModel Reference Manual - ISP

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?