MacroModel Reference Manual - ISP

Appendix D: Force-Field File Formatfield file in the form of 00 nn nn 00, where nn is some atom number. The beginning and ending00’s are wildcard atom types.D.3.4Special Notes for MM2 and MM3The MM2 field we supply is similar to but not identical with that provided by Allinger in 1987.The MM3 parameter set is the 1991 version. The stretch, bend, torsion, and off-diagonal (e.g.,stretch-bend) equations are identical with those of the authentic fields. Included in the Macro-Model fields are a number of additional parameters to handle substructures other than thoseparameterized by Allinger. Such parameters are labeled at the right end of the parameter line asA for Addition. We have followed Allinger’s protocol of distinguishing parameter quality bynoting his final values as 1 and other, less reliable ones, as 2 or 3' (also at the right of eachparameter line). When you report the results of a MacroModel MM2 or MM3 calculation, thenyou should report what nonstandard, additional parameters (if any) are used.More significant departures involve charges. MacroModel uses the partial charge (optional inMM2) treatment of electrostatics instead of the MM2/MM3 standard dipole-dipole electrostatics.Partial charges for the actual MM2 or MM3 parameters come from the classical definitionof a bond dipole and thus correspond to the MM2 or MM3 dipoles exactly. Electrostaticenergies will however be different from those given by the authentic Allinger programs andwill differ the most when the charged/dipolar groupings are close together. As we providethem, MM2 and MM3 force fields use distance-dependent dielectric electrostatics.The MacroModel implementation of MM2/MM3 includes approximate parameters forhydrogen bonds which were adjusted to mimic AMBER hydrogen bonding potentials. Part ofthe hydrogen bonding implementation included the removal of lone pairs from ester and arylether oxygens which gave too high a hydrogen bonding energy—this removal of lone pairsfrom ether oxygens bound to sp2 centers is another departure from the official MM2.Whereas MM2 and MM3 use a SCF pi calculation to obtain parameters for conjugatedsystems, MacroModel uses specific torsional parameters from the force field for conjugateddienes, enones, arenes, etc. Where available, these torsional parameters were developed to fitdata from Allinger’s papers or from MM3. Otherwise, they were developed to fit ab initio data.Aromatic ring parameters are given in the special substructure section of the field.A final relatively insignificant difference is the way out-of-plane bending is handled. In MM2and MM3, an out-of-plane distance is computed whereas in MacroModel we use an impropertorsion with a barrier which mimics the MM2/3 out of plane energy for moderate excursionsfrom planarity.210MacroModel 9.7 Reference Manual