Utils.Symmetrizers.amber_symmetrizer module

Description

This module defines the ParaMol.Utils.Symmetrizers.amber_symmetrizer.AmberSymmetrizer used to handle AMBER atom types.

class ParaMol.Utils.Symmetrizers.amber_symmetrizer.AmberSymmetrizer(top_file, xyz=None)

Bases: ParaMol.Utils.Symmetrizers.symmetrizer.Symmetrizer

ParaMol class that implements methods to symmetrize the ParaMol Force Field so that it respects AMBER atom-types.

Parameters

  • top_file (str) – AMBER prmtop file

  • xyz (str or array, optional) – If provided, the coordinates and unit cell dimensions from the provided Amber inpcrd/restart file will be loaded into the molecule, or the coordinates will be loaded from the coordinate array

save_frcmod(output_file)

Method that saves the .frcmod AMBER file with the current force field parameters of the self._amber_prmtop instance.

Notes

In order to update the self._amber_prmtop instance with the optimal parameters, the method update_term_types_parameters should be run before this one.

Parameters

output_file (str) – Name of the output file

Returns

None