MacroModel Reference Manual - ISP

MacroModel Reference ManualAppendix CAppendix C: Atom and Bond TypesC.1 The atom.typ FileMacroModel atom types are not “hard-wired” into the program, but are read in at run-timefrom a file called atom.typ. We continue to use the original MacroModel atom types for mostapplications, but now have a mechanism for easily adding new types. The list of explicitlysupported atom types has been expanded to include:Li + ,Na + ,K + ,Rb + ,Cs + ,Ca 2+ ,Ba 2+ ,Mg 2+ ,Mn 2+ ,Mn 3+ ,Mn 4+ ,Mn 5+ ,Mn 6+ ,Mn 7+ ,Fe 2+ ,Fe 3+ ,Co 2+ , Co 3+ , Ni 2+ , Ni 3+ , Cu + , Cu 2+ , Zn 2+ , Mo 3+ , Mo 4+ , Mo 5+ , Mo 6+ , and Cl - .You can add your own atom types and supply parameters for these types in the force-field file.The default atom.typ file is the one located in $SCHRODINGER/mmshare-vversion/data; alocal file of this name overrides the default, as does a local file whose name is filename.typ,where filename is the stem of the filename.mae file. This system of default version with localoverrides is analogous to that used for force field and solvation files.Currently MacroModel is parameterized to accept atom types up through number 300. Werestrict the type numbers that we supply to the range 0 through 199. When adding your owntypes, you should begin with the number 200. Negative atom types are not possible.The Maestro GUI also reads the atom.typ file, and you may change atoms in built structuresto new types (including user-defined types) from the graphical interface. However, no provisionis made in the current version for the builder to obtain the geometric information it needsfrom the atom.typ file, which would require extensions to the format of this file. Also, theoriginal atom types remain “hard-wired” in MacroModel; thus, we (again) advise users to addnew types if desired, but not to redefine types that we supply.The atom.typ file itself contains comments describing its format and usage.C.2 MacroModel Bond TypesThe following table lists the values that may appear in the MacroModel structure file formatfor bond orders, and the corresponding meaning of these values.MacroModel 9.7 Reference Manual 181