MacroModel Reference Manual - ISP

MacroModel Reference ManualAppendix DAppendix D: Force-Field File FormatD.1 Organization of the Force-Field FileForce-field parameters are obtained by MacroModel at execute time prior to performing energycalculations. Force-field parameters may be obtained from a co-process, using the BMFFmechanism (see Appendix E) or, more commonly, may be read in from a file, the force-fieldfile. This appendix describes the latter mechanism. The force-field file tells the program whichof the various possible energetic equations the particular force field uses for each type of interaction,and what the values of the parameters are (force constants, natural values of internalcoordinates, etc.) for different combinations of atoms. Making changes to the parameter setused by a calculation is simply a matter of editing the force field file to change parameters oradding new ones.See the description of the FFLD command for more information about the force fields wesupply.Force-field files have several sections:• The Introductory Section tells the program which equations and conversion factors to usein computing energies. This section also lists a variety of alternatives and selectionswhich may be chosen by making minor editing changes to the file. Finally, special atomsymbols may be defined that will be equivalenced to multiple standard atom types for theconvenience of further specification.• The Main Parameter Section contains parameters which can be assigned based on knowingthe local environment of the atoms involved in an interaction (a stretch, bend, torsionor nonbonded atom pair) out to at most a distance of two covalent bonds.• The Substructure Section contains parameters which can be assigned only by knowinghow atoms in an interaction are placed in a larger context; for example, some AMBER*parameters for atoms in standard amino acids are assigned differently in this sectiondepending on which amino acid the atom is part of.At the left of each line is a two-character field which indicates the format or contents of theline. This two-character field is most often interpreted as an integer, I, though in certain situationsit contains character data. If I is a negative number, it indicates the Fortran format forreading the group of subsequent lines, as described in Table D.1.MacroModel 9.7 Reference Manual 189