Module param_inference 

Uses reasoning similar to AnteChamber’s to estimate force field parameters using DEF files. Specifically, we use DEF_GFF2 for Gaff2 force field names, and DEF_ABCG2 for FRCMOD bonded paraemter (generally dihedral) overrides. Reference source code

Reference Antechamber config files e.g. Also review the Antechamber config files in the Amber install dir: ATOMTYPE_BCC.DEF in $AMBERHOME/dat/antechamber

Description of its parts: https://ambermd.org/antechamber/ac.html#am1bcc Of interest: -Atomtype -Bondtype -Parmchk

Structs

AmberDefSet

Note: We’ve commented out all but the ones we need for small organic molecules.

Functions

assign_missing_params

Identify all combinations of FF type in this set of atoms that requires bonded parameters. For each, check if this parameter is set in our universal small organic molecule param set (Amber’s GAFF2). If not present, apply the closest universal param to it based on force field types. todo: With correction factors?

find_ff_types

Find Amber force field types for atoms in a small organic molecule. Usese reasoning similar to Amber’s Antechamber program to assign these based on atom type, and neighboring atoms and bonds. For example, if in a ring, the nature of the ring, the elements of neighbors etc. todo: Partial charge here, or elsewhere? todo: Load

update_small_mol_params

A high level interface for param inference: Updates FF type, partial charge for each atom in a small organic molecule, and provides molecule-specfiic (FRCMOD) overrides.