qmmmrebind.parameterize.TorsionDriveParams

class qmmmrebind.parameterize.TorsionDriveParams(num_charge_atoms='', index_charge_atom_1='', charge_atom_1='', tor_dir='torsion_dir', reparameterized_torsional_params_file='reparameterized_torsional_params.txt', psi_input_file='torsion_drive_input.dat', xyz_file='torsion_drive_input.xyz', coords_file='torsion_drive_input.txt', template_pdb='guest_init_II.pdb', system_pdb='torsion_drive_input.pdb', system_sdf='torsion_drive_input.sdf', system_xml='torsion_drive_input.xml', qm_scan_file='scan.xyz', load_topology='openmm', method='L-BFGS-B', dihedral_text_file='dihedrals.txt', system_init_sdf='torsion_drive_input_init.sdf', reparameterised_system_xml_file='guest_reparameterised.xml', reparameterised_torsional_system_xml_file='guest_torsional_reparameterized.xml')[source]

A class used to parameterize the torsional parameters of the ligand by fitting the torsional parameters obtained from torsiondrive calculations.

Previously obtained reparameterized XML forcefield file did not have the torsional parameters obtained from QM calculations. The torsional parameters obtained from torsiondrive scans are fitted and a new XML forcefield file is generated.

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Variables

  • num_charge_atoms (int, optional) – Number of charged atoms in the molecule.

  • index_charge_atom_1 (int, optional) – Index of the first charged atom.

  • charge_atom_1 (int, optional) – Charge on the first charged atom.

  • tor_dir (str, optional) – Torsiondrive directory containing separate torsiondrive folders, each containing files for a separate torsiondrive calculation for a particular dihedral angle.

  • reparameterized_torsional_params_file (str, optional) – Text file containing the forcefield parameters for the ligand previously obtained without torsional reparameterization.

  • psi_input_file (str, optional) – Input file for psi4 QM engine.

  • xyz_file (str, optional) – XYZ file for ligand coordinates.

  • coords_file (str, optional) – Text file containing the XYZ coordinates of the ligand.

  • template_pdb (str, optional) – Ligand PDB with atoms beginning from 1 to be used as a template PDB to retrieve atom indices and symbols.

  • system_pdb (str, optional) – PDB file for the torsiondrive torsion scans

  • system_sdf (str, optional) – Maximum number of geometry optimization steps.

  • system_xml (str, optional) – XML force field file for the ligand.

  • qm_scan_file (str, optional) – Output scan file for the torsiondrive scans.

  • load_topology (str, optional) – Argument to specify how to load the topology. Can either be “openmm” or “parmed”.

  • method (str, optional) – Minimization method for fitting of torsional parameters.

  • dihedral_text_file (str, optional) – Dihedral information file for torsiondrive.

  • system_init_sdf (str, optional) – Ligand SDF (structure-data) format file. This file will be generated only if the ligand is charged.

  • reparameterised_system_xml_file (str, optional) – Reparameterized force field XML file obtained using openforcefield without torsional reparamaterization.

  • reparameterised_torsional_system_xml_file (str, optional) – XML force field file for the ligand obtained with torsional reparamaterization.

__init__(num_charge_atoms='', index_charge_atom_1='', charge_atom_1='', tor_dir='torsion_dir', reparameterized_torsional_params_file='reparameterized_torsional_params.txt', psi_input_file='torsion_drive_input.dat', xyz_file='torsion_drive_input.xyz', coords_file='torsion_drive_input.txt', template_pdb='guest_init_II.pdb', system_pdb='torsion_drive_input.pdb', system_sdf='torsion_drive_input.sdf', system_xml='torsion_drive_input.xml', qm_scan_file='scan.xyz', load_topology='openmm', method='L-BFGS-B', dihedral_text_file='dihedrals.txt', system_init_sdf='torsion_drive_input_init.sdf', reparameterised_system_xml_file='guest_reparameterised.xml', reparameterised_torsional_system_xml_file='guest_torsional_reparameterized.xml')[source]

Methods

__init__([num_charge_atoms, ...])

write_reparams_torsion_lines()

Saves a text file containing torsional parameters for the ligand obtained through openforcefield.

write_reparams_torsion_lines_charged()

Saves a text file containing torsional parameters for a charged ligand obtained through openforcefield.

write_torsional_reparams()

Generates a XML force field file for the ligand with reparameterized torsional parameters.