MacroModel Reference Manual - ISP

Appendix D: Force-Field File Formatwhere ν is the IR frequency in wave numbers (cm -1 ), and M 1and M 3are the atomic masses ofthe first and third atoms involved in the bend. AMBER bending constants are approximately120 times those given in MM2 or MM3 for the same bending array.While stretch (and sometimes bend) parameters may be moved from one force field to anotherwithout creating large errors, torsional parameters are highly force field dependent for thesame array of atoms. Consequently, new torsions must be parameterized in the context of thefield to be used. Often, data from one well-parameterized force field (e.g., MM2 or MM3) canbe used as the basis for parameterization of another force field.Nonbonded parameters for unusual atoms may be approximated according to the followingequation [50, 51]. The van der Waals ε is given by:ε = 1.4154 α 2 r –6 (α/N el ) -1/2where r is the covalent radius (ionic radius for ions) in Angstroms, α is its polarizability (Å 3 )and N el is its effective number of electrons for the atom (generally equal to the actual numberof electrons for first and second row elements).While these protocols work well, it is easy to corrupt the force field by careless addition of newparameters or modifications of old ones. If you make any additions to the force fields, be sureand test that the additions you make do not change the energetic results of a adequately widevariety of test structures. In particular, unless it is your intent to have your new parameters altereven the structures which are well parameterized with the force-field as we supply it, youshould check to make sure that the energy tests described in Appendix A still work properly.D.3.3Special Notes for AMBERAMBER94 does not differ from the published force-field in any significant way.The MacroModel implementation of AMBER* is identical to original AMBER with theexception of additional parameters which we have added. We supply the field by default with aconstant dielectric treatment, the united-atom AMBER charge set and Kollman’s 6,12-LennardJones hydrogen bonding treatment. Other options (e.g., distance dependent dielectric) may beset by modifying the first section of the AMBER force field file or via button selections fromwithin MacroModel.The AMBER force field we supply has a special substructure notation, which allows a singleresidue substructure to match both united atom and all atom structures and assign the appropriatecharges as well as other parameters. Although the linear notation gives only the unitedatom description of the molecule, the program will interpret the notation both as an actualunited atom representation and as the all atom representation with the appropriate number ofexplicit hydrogens. The charges given for the residues are in the united atom representation forMacroModel 9.7 Reference Manual 207