The atom.typ File

MacroModel atom types are not “hard-wired” into the program, but are read in at run-time from a file called atom.typ. We continue to use the original MacroModel atom types for most applications, but now have a mechanism for easily adding new types. The list of explicitly supported atom types has been expanded to include a large number of types for various cations and anions as well as other elements.

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; a local 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 local overrides is analogous to that used for force field and solvation files.

Currently MacroModel is parameterized to accept atom types up through number 300. We restrict the type numbers that we supply to the range 0 through 199. When adding your own types, 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 structures to new types (including user-defined types) from the graphical interface. However, no provision is made in the current version for the builder to obtain the geometric information it needs from the atom.typ file, which would require extensions to the format of this file. Also, the original atom types remain “hard-wired” in MacroModel; thus, we (again) advise users to add new types if desired, but not to redefine types that we supply.

The atom.typ file itself contains comments describing its format and usage.