MacroModel Reference Manual - ISP

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Appendix D: Force-Field File Formatyour entry at the top of the appropriate section (stretch, bend, etc.). You should also rerun theenergy test structures supplied to be sure you have not changed other parameters in error. Alsobe sure to make the appropriate changes in the interaction descriptors at the far right of eachentry so that the parameter set will be correctly identified (as we have defined them) as(Column 1) O (original), M (modified), or A (added), and as (Column 2) 1 (high quality parameter),2 (tentative parameter) or 3 (generalized parameter). We also add a brief comment andthe name of (or reference to) the parameter author. You should add the appropriate comments,your initials and location for each entry you add or modify to keep track of the parameters youhave added. You will want to be able to add your new parameters to any force fields we supplyin the future. Note that force field lines are up to 130 characters so set your editor to display theentire line.Some excerpts from mm2.fld follow, by way of example. Figure D.2 on page 201 exhibitsseveral stretch interactions.A positive bond moment makes the first atom listed in the bond entry positively charged. In thefourth entry above, the value of –0.32 Debye makes the C3 negative and the H1 positive.In the first line of the stretch section, a special C3 - C3 interaction is defined by the optionalalpha descriptors O3O3 which require that both the first C3 and the second C3 have attachedO3s, as in ethylene glycol. This is not a standard MM2 stretch and is therefore marked in theSEL 1 field with an A. The SEL 2 field is marked 1 since the parameter is a high quality one.The second and third lines contain MM2 and MM2' parameters, and are distinguished at theright hand end of the lines in the labeling of the second line by the ALT specifications 1 a and1 b.As described above, if ALT 1 is given the a value in the Introductory Section of the force field,MM2 (not MM2’) parameters will be used.Some bend parameters are shown in Figure D.3 on page 201. The first few parameters shownare original (O), high quality (1) MM2 parameters. Also, the environmental dependence of thebending angles (methyl vs. methylene vs. methyne) is handled with optional descriptors for thecentral atom. The last few parameters shown are highly generalized bend interactions aboutvarious sorts of central atoms. The use of wild-card atom types (00) and bond types (*) meansthat one of these interactions will match nearly any bend having the given central atom. Theseare given at the end of the bend section, so that more specific interactions will match first.These entries are labeled A (added) and 3 (low quality).A portion of the stretch-bend part of the force-field is shown in Figure D.4 on page 202.Torsions are shown in Figure D.5 on page 202. The same considerations hold for these interactiontypes as hold for stretches and bends. Of course, not all force fields have all interactiontypes; for example, the AMBER force fields have no stretch-bend interactions.200MacroModel 9.7 Reference Manual
Appendix D: Force-Field File FormatFigure D.2.C Stretching Interactions (STR) Opt. Descriptor Parameter ReferencingC ---------- ------------ ---- ---------- --------- ----- -----------------------C Bond Length Constant Bond Moment Atm1 Atm2 Select AltrnC (ang) (mdyn/ang) (debye) 1 2 3 4 5 S A Comment21 C3 - C3 1.5150 4.4000 0.0000 O300 O300 A 1 C(-O)-C(-O), WCS (CU)1 C3 - C3 1.5230 4.4000 0.0000 0000 0000 O 1 1 a C-C1 C3 - C3 1.5260 4.4000 0.0000 0000 0000 M 1 1 b C-C, MM2', Tet, 2769 (83)1 C3 - H1 1.1130 4.6000 -0.3200 Cl00 0000 A 1 H-C(-Cl), WCS (CU)1 C3 - H1 1.1130 4.6000 -0.7500 N500 0000 A 2 H-C(-N+), WCS (CU)Figure D.3.C Bending Interactions (BND) Opt. DescriptorsC ------- ------------ ---- -----------C Angle Bending Constant Atm1 Atm2 Atm3C (deg) (mdyn/rad**2)22 H1 - C3 - H1 109.4700 0.3200 0000 H1H1 0000 O 1 H-C(H2)-H2 H1 - C3 - H1 109.0000 0.3200 0000 H100 0000 O 1 H-C(H)-H2 H1 - C3 - H1 109.4000 0.3200 0000 0000 0000 O 1 H-C-H2 C3 - C3 - C3 109.5000 0.4500 0000 H1H1 0000 O 1 C-C(H2)-C2 C3 - C3 - C3 109.5100 0.4500 0000 H100 0000 O 1 C-C(H)-C2 C3 - C3 - C3 109.4700 0.4500 0000 0000 0000 O 1 C-C-C2 C3 - C3 - H1 110.0000 0.3600 0000 H1H1 0000 O 1 C-C(H2)-H..2 00 * C3 * 00 110.0000 0.4500 0000 0000 0000 A 3 -C(sp3)-, WCS (CU)2 00 * C2 * 00 120.0000 0.4500 0000 0000 0000 A 3 -C(sp2)-, WCS (CU)2 00 * C1 * 00 180.0000 0.4000 0000 0000 0000 A 3 -C(sp)-, WCS (CU)MacroModel 9.7 Reference Manual 201
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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
Page 207: Appendix D: Force-Field File Format
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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