MacroModel Reference Manual - ISP

Appendix D: Force-Field File FormatD.4 Substructure SectionD.4.1Use of SubstructuresThe last section of the force field file lists special substructures. A force-field substructure is acontiguously connected chemical entity, such as an amino-acid residue or an aromatic nucleus.The connectivity is given by a simple linear notation. For each substructure, parameters aregiven that override any parameters obtained for the corresponding interactions from the MainParameter Section of the force-field. These parameters may lie wholly within the substructureor they may include off-substructure atoms. Single-atom van der Waals parameters may not bespecified within substructures and charges may be specified either by means of bond dipoles,as in the Main Parameter Section, or else by means of explicit charges. In contrast to the MainParameter Section of the force-field, parameters for special substructures must be entered withthe most specific parameters last, rather than first; in other words, the last parameter matchfound is the one that is used. This is also true for the substructure matching process: if a givenportion of the molecule under study is matched by several force-field substructures, thesubstructure that appears last in the force field is normally used. For substructure matching, butnot for parameter matching within substructures, this behavior may be overridden in the forcefieldspecification of the substructure.Within the Substructure Section of the force-field, lines with I>0 or beginning with characterdata have the following meanings; this list augments the values in the Main Parameter Section.Recall that I is a two-character field; single values shown must be right-aligned in this field.8 Constants for charges in special substructures.9 Substructure linear notation (see section below).CaTanData lines beginning with a blank followed by a C or S mean “continue” or “stop” inthe substructure-matching process.Data lines beginning with two ASCII characters (e.g., aT or aR) indicate a geometricalconstraint line, as described in the Geometry Dependent Parameters Section.Data lines beginning with a character followed by an integer encode interactionssubjected to geometry dependence, as described in the Geometry Dependent ParametersSection. The letter refers to the corresponding geometric constraint line andthe integer specifies the interaction type (e.g., 1 for stretch) as usual.Note: Single-atom van der Waals parameters may not appear in substructures.Note: Partial charge line(s) in force field substructures (specified by the 8 flag in the first twocolumns) must be the last line(s) in the substructure, that is, lines for other interactionMacroModel 9.7 Reference Manual 211