MacroModel Reference Manual - ISP

Appendix D: Force-Field File FormatThe atoms in the substructure are referred to by number when parameters are assigned. Anatom is simply referred to by its position in the linear notation; for example, the serine nitrogenwould be number one and the carbonyl oxygen would be number 8.D.4.3Substructure Charge ProcessingYou can continue to specify explicit partial charges in force field substructures by specifying 8in the first two columns of a line containing such partial charges as in previous versions ofMacroModel. However, internal processing of these charges was changed in version 8.0.Whereas MacroModel used to directly “paste” such partial charges onto the system beingsimulated, it now proceeds as follows:1. Formal charges from atom.typ are assigned to the atoms in the force field substructure(DEBG 11 causes formal charges to be assigned from the .fld file).2. Such formal charges are delocalized over other atoms in that force field substructure ifappropriate.3. The delocalized formal charges are subtracted from the user specified partial charges.4. These modified partial charges are decomposed into bond charge increments.Internally, all charge processing to determine partial charges on the system being simulated isdone using bond charge increments and delocalized formal charges. For detailed output to the.log file of this process, specify DEBG 128 at the top of your .com file. Note that if wildcardatom types (e.g., N0, O0, 00) or generalized atom types (e.g., C, O) are used in the substructurelinear notation, such atoms will be assigned formal charges of 0.0, and formal charge delocalizationwill not be allowed over those atoms in the delocalized formal charge calculation forthat force field substructure. Additionally, formal charge delocalization will not be done overwildcard bond types, denoted by “*” in the substructure linear notation. If equivalenced atomtypes are used in the force field substructure, the formal charge properties will be taken to bethose for the first MacroModel atom type in the list of atom types for that particular equivalencedatom type. For example, given the line1 CS CA CB CCthe formal charge properties for an atom of type CS in a force field substructure will be thosewhich are specified for the actual MacroModel atom type CA.D.4.4Substructure ExamplesThe following example shows a substructure specification for a cyclopropane nucleus. The -3and -2 that appear alone on lines specify the format for the reading of subsequent lines. The C,9, 1, 2, etc. introducing other lines specify the nature of the information to be read. The C specifiesthat the title of a substructure is to be read, with the default (“continue”) matching214MacroModel 9.7 Reference Manual