MacroModel Reference Manual - ISP

Appendix D: Force-Field File Formatbehavior; an S (“stop”) in place of C would prevent the matched atoms in the structure beingstudied from being candidates for further substructure matches. In other words, S would overridethe “use last substructure match” default behavior for this particular substructure. 9 introducesa linear substructure specification within the -3 format block and 1, 2, etc. introduceparameter specifications as follows, within the -2 format block.-3C Cyclopropanoid9 C3-C3-00-1-21 1 2 1.5010 4.4000 0.00001 1 C2 1.4670 4.4000 -0.15001 1 C3 1.5050 4.4000 0.15001 1 H1 1.0860 4.6000 0.00002 1 2 3 60.0000 0.45002 1 2 H1 119.7000 0.36002 1 2 C3 118.2000 0.60002 1 2 C2 118.2000 0.60002 H1 1 H1 120.6000 0.32002 C3 1 H1 123.5000 0.36002 C3 1 C3 120.0000 0.45002 1 C3 C3 112.4000 0.45004 1 2 C3 H1 0.0000 0.0000 0.12004 1 2 C3 C3 0.3000 0.0000 0.45004 C3 1 C3 H1 0.0000 0.0000 0.69004 H1 1 C3 H1 0.0000 0.0000 0.69004 C3 1 C3 C3 0.0000 0.0000 0.00004 H1 1 C3 C3 0.0000 0.0000 0.2670Substructure interaction lines can specify optional connected atoms, but if they do, then nonwildcardatom-types in the optional-atom list will be matched only against atoms not in thesubstructure. In this context, a wildcard atom-type is either 00, which matches any atom type,or else one of the wildcard types for an element; for example, C0 for any carbon. The numbersin the interaction proper (such as 1 2 in the first stretch shown) correspond to the numbers inthe linear substructure notation. Atom types, when shown, correspond to matching atoms offthe substructure.The following example shows a substructure for benzenoids, giving benzene-like bond lengths,angles, and force constants. Wild-card bond types are used to allow matching of any resonanceform. Since the substructure is matched a total of 12 different ways, all aromatic bonds will beparameterized by this substructure (with length = 1.39 Å, force constant = 8.0667), etc. Thetorsion is generalized (the first and last entries are 00, the wild-card atom type), so it representsthe total barrier (recall that this handling is special for generalized torsions in substructures).The barriers used by the individual components would thus be V 2 = 36.8/4 kcal/mol.-3MacroModel 9.7 Reference Manual 215