MacroModel Reference Manual - ISP

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Appendix D: Force-Field File FormatFigure D.4.C Stretch Bend Interactions (S-B) Opt. DescriptorC ------- ---- ------------ ---- ----------C Str Bend Const Atm1 Atm2 Atm3-23 H1 * C1 * 00 0.0900 0000 0000 0000 O 1 H-C(sp)*3 00 * C1 * 00 0.1200 0000 0000 0000 O 1 *C(sp)*3 H1 * C2 * 00 0.0900 0000 0000 0000 O 1 H-C(sp2)*3 H1 * C2 . 00 0.0900 0000 0000 0000 O 1 H-C(sp2).3 00 * C2 * 00 0.1200 0000 0000 0000 O 1 *C(sp2)*Figure D.5.C Torsional Interactions (TOR) Opt. DescriptorC --------- ------------ ---- ----------C V1 V2 V3 Atm1 Atm2 Atm3 Atm4C (V1, V2 & V3 in kcal/mole)-24 H1 - C3 - C3 - H1 0.0000 0.0000 0.2370 0000 0000 0000 0000 O 1 1 a H-C-C-H4 H1 - C3 - C3 - H1 0.0000 0.0000 0.3500 0000 0000 0000 0000 M 1 1 b H-C-C-H MM2', Tet, 2769 (83)4 C3 - C3 - C3 - H1 0.0000 0.0000 0.2670 0000 0000 0000 0000 O 1 C-C-C-H4 C3 - C3 - C3 - C3 0.2000 0.2700 0.0930 0000 0000 0000 0000 O 1 1 a C-C-C-C202MacroModel 9.7 Reference Manual
Appendix D: Force-Field File FormatLow quality (3) torsional parameters are the most likely to give incorrect results in molecularmechanics. If generalized torsions are used in a calculation, then quantitative results should notbe expected and new torsional parameters should be devised to fit the molecule on the basis ofexperimental (or ab initio quantum-mechanical) data. Minimally, the results of a calculationwith low quality torsion should be compared with experimental data to determine how poor thecalculation is. See the MacroModel Technical Manual for some comments regarding parameterderivation.Figure D.6 on page 204 shows an excerpt from the section of the force-field giving out-ofplanebending parameters. When the these interactions are handled using improper torsions,the atoms are listed with the central atom (e.g., the carbon of a carbonyl group) first in theentry; that is, if the atoms are listed in this section in the sequence ABCD, the dihedral anglecalculated will really be BACD. When these interactions are being handled using Wilson angles,the two “anchor” atoms are given first, then the “apex” atom, then the “end” atom (Wilson, E.B.; Decius, J. C.; and Cross, P. C. Molecular Vibrations; Dover Publications; New York, NY,1955; p. 59).A section of the van der Waals portion of the force field is shown in Figure D.7 on page 204.This section gives single-atom van der Waals parameters which will be combined using somecombing rule. The parameters given are r 0 and ε.Note the use of optional atoms to distinguish MM2 atom types and the Lp descriptor at theright to indicate which atoms get lone pairs; for example, an O3 not bound to P, S or C(sp2) getsa lone pair. MacroModel does not use lone pairs on enol, ether or ester oxygens this givesbetter results with hydrogen bonding. In the past it was not possible to specify beta atoms forthis portion of the force field, but this is now allowed.Formal charges for atom types are obtained from the atom.typ file, rather than from thissection of the force-field file.Following the van der Waals parameters, there are two more parts of the Main InteractionSection of the force field. Figure D.8 on page 205 shows some of the special van der Waalsinteractions. These encode overrides of the normal van der Waals combining rules for atomtypepairs. Figure D.9 on page 205 shows some hydrogen-bonding parameters. Even whenthere is no special functional form invoked for hydrogen bonding, the parameters for whateverstandard nonbonded potential is being used is derived from this section for atoms that canhydrogen bond.MacroModel 9.7 Reference Manual 203
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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
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Page 231 and 232: Appendix E: The BMFF ProtocolBefore
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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
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