MacroModel Reference Manual - ISP

Appendix D: Force-Field File FormatC Benzenoids (Beckhaus, ChemBer, 116, 86 (1983))9 C2*C2*AA*AA*AA*AA*1-21 1 2 1.3900 8.0667 0.00002 1 2 3 120.0000 0.43004 00 1 2 00 0.0000 36.8000 0.0000The usual torsional parameter handling in substructures is that all parameters (V 1 ,V 2 , and V 3 )for a matched torsional interaction are overwritten by the torsional parameters from a torsionalsubstructure parameter line. It is possible to overwrite only specific components (e.g., only theV 2 component) by using the special parameter entry 99.9999 for the other components; thisprevents overwriting. For example, the torsional parameter line below would replace only theV 2 barrier (with 2.5 kcal/mol) of an existing torsional interaction.4 00 2 3 00 99.9999 2.5000 99.9999Note again that the V 2 barrier specified here is the total barrier, because of the use of wild-cardatom types.Figure D.10 on page 217 shows how a specific set of charges (perhaps derived from ab initioquantum-mechanical studies) can be specified directly in a substructure. The purpose of thesubstructure above is to load the partial charges given in the line beginning 8. The charges areplaced on the substructure atoms in the order in which the atoms appear in the substructurenotation. When using partial charges directly instead of bond dipoles, be sure that the totalcharge of the substructure sums to 0.0 for neutral substructures. Also check the final charge setusing Maestro (the Electrostatics panel) to test your charge data.D.4.5Geometry-dependent ParametersIt is occasionally desirable to make the parameters used for certain degrees of freedom dependentupon the geometry of some other degree of freedom. We allow this, in a limited sense.First, the degree of freedom which dictates the parameters must be configurational; that is, wedo not provide a mechanism for “on-the-fly” reparameterization of atoms, but only for parameterizingsome degree of freedom based on the initial value of some other. Second, we providethree specific forms of this dependence. First of all, a parameter for an interaction can dependon a torsion value, and secondly a parameter for an interaction can depend on whether theinteraction is within a ring; finally, a parameter can depend on the initial value of an angle. Thefollowing examples illustrate several cases.216MacroModel 9.7 Reference Manual