htmd.builder.noncanonical module

htmd.builder.noncanonical.parameterizeNonCanonicalResidues(cifs, outdir, forcefield='GAFF2', calculator=None, charge_model='AM1-BCC', is_nterm=False, is_cterm=False)

Parameterize non-canonical residues.

Parameters:

• cifs (str or list of str) – Path to the CIF file(s) containing the non-canonical residues.

• outdir (str) – Path to the output directory.

• forcefield (str, optional) – Force field to use for parameterization. Default is “GAFF2”.

• calculator (str, optional, choices: ["xTB", "AIMNet2", "ANI-1x", "ANI-2x", "ANI-1ccx", "None"]) – Energy calculator to use for fitting dihedral profiles

• charge_model (str, optional, choices: ["AM1-BCC", "Gasteiger", "Espaloma", "ESP", "RESP-PSI4", "None"]) – Charge model to use for parameterization

• is_nterm (bool, optional) – Whether the residue is a terminal N-term

• is_cterm (bool, optional) – Whether the residue is a terminal C-term