qmmmrebind.parameterize.PrepareGaussianHostGuest

class qmmmrebind.parameterize.PrepareGaussianHostGuest(charge=0, multiplicity=1, guest_pdb='guest_init_II.pdb', host_qm_pdb='host_qm.pdb', n_processors=12, memory=50, functional='B3LYP', basis_set='6-31G', optimisation='', frequency='', add_keywords_I='INTEGRAL=(GRID=ULTRAFINE)', add_keywords_II='POP(MK,READRADII)', add_keywords_III='IOP(6/33=2,6/42=6) SCRF=PCM', gauss_system_out_file='system_qm.out', fchk_system_out_file='system_qm_fchk.out', host_guest_input='host_guest.com', qm_guest_charge_parameter_file='guest_qm_surround_charges.txt', qm_host_charge_parameter_file='host_qm_surround_charges.txt', qm_guest_atom_charge_parameter_file='guest_qm_atom_surround_charges.txt')[source]

A class used to prepare the QM engine input file (Gaussian) for the receptor - ligand complex and run the QM calculations with the appropriate keywords.

This class contain methods to write an input file (.com extension) for the QM engine for the receptor - ligand complex. It then runs a QM calculation with the given basis set and functional. Checkpoint file is then converted to a formatted checkpoint file. Output files (.log, .chk, and .fhck) will then be used to extract charges for the ligand and the receptor.

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Variables

  • charge (int, optional) – Total charge of the receptor - ligand complex.

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

  • guest_pdb (str, optional) – Ligand PDB file with atom numbers beginning from 1.

  • host_qm_pdb (str, optional) – PDB file for the receptor’s QM region.

  • n_processors (int, optional) – Number of processors to be used for Gaussian program to run and set in %NProcShared command of Gaussian.

  • memory (int, optional) – Memory (in GB) to be used set in %Mem command of Gaussian.

  • functional (str, optional) – Exchange/Correlation or hybrid functional to use in the Gaussian QM calculation.

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

  • optimisation (str, optional) – set to “OPT” to perform a geometry optimization on the ligand specified in the system; else set to an empty string.

  • frequency (str, optional) – set to “FREQ” for Gaussian to perform a frequency calculation; else set to an empty string.

  • add_keywords_I (str, optional) – Specifies the integration grid.

  • add_keywords_II (str, optional) – Specifies the QM engine to select one of the methods for analyzing the electron density of the system. Methods used are based on fitting the molecular electrostatic potential. Methods used are : POP=CHELPG (Charges from Electrostatic Potentials using a Grid based method) and POP=MK (Merz-Singh-Kollman scheme)

  • add_keywords_III (str, optional) – Used to include the IOp keyword (to set the internal options to specific values) in the Gaussian command.

  • gauss_system_out_file (str, optional) – This file contains the output script obtained after running the Gaussian QM calculation.

  • fchk_system_out_file (str, optional) – Formatted checkpoint file obtained from the checkpoint file using formchk command.

  • host_guest_input (str, optional) – Gaussian input file (.com extension) for the receptor - ligand QM region.

  • qm_guest_charge_parameter_file (str, optional) – File containing the charges of ligand atoms and their corresponding atoms. Charge obtained are the polarised charged due to the surrounding receptor’s region.

  • qm_host_charge_parameter_file (str, optional) – File containing the charges of the QM region of the receptor.

  • qm_guest_atom_charge_parameter_file (str, optional) – File containing the charges of ligand atoms. Charge obtained are the polarised charged due to the surrounding receptor’s region.

__init__(charge=0, multiplicity=1, guest_pdb='guest_init_II.pdb', host_qm_pdb='host_qm.pdb', n_processors=12, memory=50, functional='B3LYP', basis_set='6-31G', optimisation='', frequency='', add_keywords_I='INTEGRAL=(GRID=ULTRAFINE)', add_keywords_II='POP(MK,READRADII)', add_keywords_III='IOP(6/33=2,6/42=6) SCRF=PCM', gauss_system_out_file='system_qm.out', fchk_system_out_file='system_qm_fchk.out', host_guest_input='host_guest.com', qm_guest_charge_parameter_file='guest_qm_surround_charges.txt', qm_host_charge_parameter_file='host_qm_surround_charges.txt', qm_guest_atom_charge_parameter_file='guest_qm_atom_surround_charges.txt')[source]

Methods

__init__([charge, multiplicity, guest_pdb, ...])

get_fchk()

Converts the Gaussian checkpoint file (.chk) to a formatted checkpoint file (.fchk).

get_qm_host_guest_charges()

Extract charge information for the receptor - ligand QM region.

run_gaussian()

Runs the Gaussian QM calculation for the ligand - receptor region locally.

write_input()

Writes a Gaussian input file for the receptor - ligand QM region.