qmmmrebind.parameterize.TorsionDriveSims

class qmmmrebind.parameterize.TorsionDriveSims(charge=0, multiplicity=1, reparameterised_system_xml_file='guest_reparameterised.xml', torsion_xml_file='guest_torsion_xml.txt', xyz_file='guest_coords.xyz', psi_input_file='torsion_drive_input.dat', memory=50, basis_set='6-31G', functional='B3LYP', iterations=2000, method_torsion_drive='native_opt', system_bonds_file='guest_bonds.txt', tor_dir='torsion_dir', dihedral_text_file='dihedrals.txt', template_pdb='guest_init_II.pdb', torsion_drive_run_file='run_command', dihedral_interval=15, engine='psi4', energy_threshold=1e-05)[source]

A class used to create a filetree for torsion scan using torsionsdrive for the dihedral angles of the ligand.

This class creates a directory for carrying out torsiondrive calculations followed by fitting of torsional parameters. Methods in this class are used to run torsiondrive calculations either for all of the torsional angles, or for non-hydrogen / heavy atoms contributing to the torsional angle.

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Variables

  • charge (int, optional) – Charge of the ligand.

  • multiplicity (int, optional) – Spin Multiplicity (2S+1) of the ligand where S represents the total spin of the ligand.

  • reparameterised_system_xml_file (str, optional) – Reparamaterixed XML force field for the ligand.

  • torsion_xml_file (str, optional) – A text file containing torsional parameters from reparameterised XML file.

  • xyz_file (str, optional) – XYZ file containing the coordinates of the guest molecule.

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

  • memory (int, optional) – Memory (in GB) to be used.

  • basis_set (str, optional) – Basis set to use for the QM engine.

  • functional (str, optional) – Exchange/Correlation or hybrid Functional for the QM engine.

  • iterations (int, optional) – Maximum number of geometry optimization steps.

  • method_torsion_drive (str, optional) – The algorithm/package to use while running the torsiondrive scan. Using –native_opt uses QM program native constrained optimization algorithm and turns off geomeTRIC package.

  • system_bonds_file (str, optional) – Text file containing bond parameters for the ligand.

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

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

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

  • torsion_drive_run_file (str, optional) – bash file for torsiondrive calculations.

  • dihedral_interval (int, optional) – Grid spacing for dihedral scan, i.e. every n degrees (where n is an integer), multiple values will be mapped to each dihedral angle.

  • engine (str, optional) – Engine for running torsiondrive scan.

  • energy_threshold (float, optional) – Only activate grid points if the new optimization is lower than the previous lowest energy (in a.u.).

__init__(charge=0, multiplicity=1, reparameterised_system_xml_file='guest_reparameterised.xml', torsion_xml_file='guest_torsion_xml.txt', xyz_file='guest_coords.xyz', psi_input_file='torsion_drive_input.dat', memory=50, basis_set='6-31G', functional='B3LYP', iterations=2000, method_torsion_drive='native_opt', system_bonds_file='guest_bonds.txt', tor_dir='torsion_dir', dihedral_text_file='dihedrals.txt', template_pdb='guest_init_II.pdb', torsion_drive_run_file='run_command', dihedral_interval=15, engine='psi4', energy_threshold=1e-05)[source]

Methods

__init__([charge, multiplicity, ...])

create_non_H_bonded_torsion_drive_dir()

Creates a directory for carrying out torsiondrive calculations for all non-hydrogen bonded torsional angles.

create_non_H_torsion_drive_dir()

Creates a directory for carrying out torsiondrive calculations for all non-hydrogen torsional angles.

create_torsion_drive_dir()

Creates a directory for carrying out torsiondrive calculations for all the proper dihedral angles.

run_torsion_sim()

Run torsion scans using torsiondrive locally.

write_psi4_input()

Writes a psi4 input QM file.

write_tor_params_txt()

Saves a text file containing torsional parameters from the reparameterized XML force field file.

write_torsion_drive_run_file()

Saves a bash file for running torsion scans for torsiondrive.