ProtoCaller.Parametrise.amber module

ProtoCaller.Parametrise.amber.amberWrapper(params, filename, molecule_type, id=None, charge=None, *args, **kwargs)

Parametrises an input file according to AMBER force field.

Parameters

  • params (ProtoCaller.Parametrise.Params) – Force field parameters.

  • filename (str) – Name of the input file.

  • molecule_type (str) – The type of the molecule. One of: “protein”, “ligand”, “cofactor”, “water”, “simple_anion”, “complex_anion”, “simple_cation”, “complex_cation”.

  • id (str) – The name of the molecule. Default: equal to molecule_type.

  • charge (bool) – The net charge of the molecule. Default: automatic detection by antechamber.

  • args – Positional arguments to be passed to the relevant wrapper.

  • kwargs – Keyword arguments to be passed to the relevant wrapper.

Returns

files – The output parametrised file(s). If there is more than one file, the first one is always the topology file and the second one - the coordinate file.

Return type

[str]

ProtoCaller.Parametrise.amber.runAntechamber(force_field, file, output_ext='mol2', charge=None)

A wrapper around antechamber.

Parameters

  • force_field (str) – Which force field to use. Only “gaff” and “gaff2” are accepted.

  • file (str) – Name of input file.

  • output_ext (str) – Output extension.

  • charge (int) – The net charge of the molecule. Default: automatic detection by antechamber.

Returns

output_name – Absolute path of the output parametrised file.

Return type

str

ProtoCaller.Parametrise.amber.runParmchk(force_field, file)

A wrapper around parmchk2.

Parameters

  • force_field (str) – Which force field to use. Only “gaff” and “gaff2” are accepted.

  • file (str) – Name of the file generated by antechamber.

Returns

filename_output – Absolute path to the extra parameter file generated by parmchk2.

Return type

str

ProtoCaller.Parametrise.amber.runTleap(force_fields=None, files=None, param_files=None, id=None, disulfide_bonds=None)

Writes and runs tleap scripts.

Parameters

  • force_fields ([str]) – All force fields to be loaded in tleap.

  • files ([str]) – All regular files to be loaded in tleap.

  • param_files ([str]) – All parameter files to be loaded in tleap.

  • id (str) – The name of the molecule. Default: equal to molecule_type.

  • disulfide_bonds ([[ProtoCaller.IO.PDB.Residue, ProtoCaller.IO.PDB.Residue]]:) – Residues between which there is a disulfide bond.

Returns

filenames – Absolute paths of the final parametrised files. The first file is a topology file and the second file is a coordinate file.

Return type

[str]