mstk.forcefield.typer.GaffTyper

class mstk.forcefield.typer.GaffTyper(file=None)

GaffTyper is specifically designed for GAFF atom type assignment. It should only be used with the type definition file gaff.zft

Compared with ZftTyper, this class will handle conjugated atom types according to the GAFF convention, e.g. cc/cd, ce/cf etc…

The official tool for GAFF - antechamber has plenty of issues: - Mysterious aromatic assignment - A lost of parameters missing. parmchk2 gives unreasonable guess for torsion parameters, e.g. biphenyl

Parameters:

file (str or file-like object, optional) – Type definition file. If the file does not exist, will search it under directories defined by MSTK_FORCEFIELD_PATH.

Notes

  • SMARTS is parsed by using RDKit package. Make sure it is installed.

  • In type definition file, empty lines are ignored, and comments should start with ##.

Methods

__init__([file])

type(top_or_mol)

Assign types for all atoms in a topology or molecule.