qmmmrebind.parameterize.HostAmberXMLAmber

class qmmmrebind.parameterize.HostAmberXMLAmber(system_pdb='host.pdb', system_sdf='host.sdf', charge=0, system_mol2='host.mol2', system_in='host.in', system_frcmod='host.frcmod', prmtop_system='host.prmtop', inpcrd_system='host.inpcrd', system_leap='host.leap', system_xml='host.xml', sim_output='sim_output.pdb', sim_steps=1000, charge_parameter_file='host_qm_surround_charges.txt', system_qm_pdb='host_qm.pdb', bond_parameter_file='host_qm_bonds.txt', angle_parameter_file='host_qm_angles.txt', system_qm_params_file='host_qm_params.txt', reparameterised_intermediate_system_xml_file='host_intermediate_reparameterised.xml', system_xml_non_bonded_file='host_xml_non_bonded.txt', system_xml_non_bonded_reparams_file='host_xml_non_bonded_reparams.txt', reparameterised_system_xml_file='host_reparameterised.xml', non_reparameterised_system_xml_file='host.xml', prmtop_system_non_params='host_non_params.prmtop', inpcrd_system_non_params='host_non_params.inpcrd', prmtop_system_params='host_params.prmtop', inpcrd_system_params='host_params.inpcrd', load_topology='openmm')[source]

A class used to generate a template force field XML file for the receptor in order regenerate the reparameterised forcefield XML file.

This class contain methods to generate a template XML force field through openforcefield. Re-parameterized XML force field files are then generated from the template files. Different energy components such as bond, angle, torsional and non-bonded energies are computed for the non-reparametrized and the reparameterized force fields. Difference between the non-reparameterized and reparameterized force field energies can then be analyzed. …

Variables

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

  • system_sdf (str, optional) – Receptor SDF (structure-data) format file.

  • charge (int) – Charge of the ligand.

  • system_mol2 (str, optional) – Receptor Mol2 file obtained from PDB file.

  • system_in (str, optional) – Prepi file as required by antechamber.

  • system_frcmod (str, optional) – FRCMOD file as required by antechamber.

  • prmtop_system (str, optional) – Topology file obtained from the receptor PDB.

  • inpcrd_system (str, optional) – Coordinate file obtained from the receptor PDB using the command saveamberparm.

  • system_leap (str, optional) – Amber generated leap file for generating and saving topology and coordinate files.

  • system_xml (str, optional) – Serilazed XML force field file of the receptor.

  • sim_output (str, optional) – PDB file containing the trajectory coordinates for the OpenMM simulation.

  • sim_steps (str, optional) – Number of steps in the OpenMM MD simulation.

  • charge_parameter_file (str, optional) – File containing the charges of receptor atoms and their corresponding atoms.

  • system_qm_pdb (str, optional) – Receptor QM region’s PDB file with atom numbers beginning from 1.

  • bond_parameter_file (str, optional) – Text file containing the bond parameters for the receptor.

  • angle_parameter_file (str, optional) – Text file containing the angle parameters of the receptor.

  • system_qm_params_file (str, optional) – A text file containing the QM obtained parameters for the receptor.

  • reparameterised_intermediate_system_xml_file (str, optional) – XML force field file with bond and angle parameter lines replaced by corresponding values obtained from the QM calculations.

  • system_xml_non_bonded_file (str, optional) – Text file to write the NonBondedForce Charge Parameters from the non-parameterised system XML file.

  • system_xml_non_bonded_reparams_file (str, optional) – Text file containing the non-bonded parameters parsed from the XML force field file.

  • reparameterised_system_xml_file (str, optional) – Reparameterized force field XML file obtained using openforcefield.

  • non_reparameterised_system_xml_file (str, optional) – Non-reparameterized force field XML file obtained using openforcefield.

  • prmtop_system_non_params (str, optional) – Amber generated topology file saved from the non-reparameterized force field XML file for the receptor.

  • inpcrd_system_non_params (str, optional) – Amber generated coordinate file saved from the non-reparameterized force field XML file for the receptor.

  • prmtop_system_params (str, optional) – Amber generated topology file saved from the reparameterized force field XML file for the receptor.

  • inpcrd_system_params (str, optional) – Amber generated coordinate file saved from the reparameterized force field XML file for the receptor.

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

__init__(system_pdb='host.pdb', system_sdf='host.sdf', charge=0, system_mol2='host.mol2', system_in='host.in', system_frcmod='host.frcmod', prmtop_system='host.prmtop', inpcrd_system='host.inpcrd', system_leap='host.leap', system_xml='host.xml', sim_output='sim_output.pdb', sim_steps=1000, charge_parameter_file='host_qm_surround_charges.txt', system_qm_pdb='host_qm.pdb', bond_parameter_file='host_qm_bonds.txt', angle_parameter_file='host_qm_angles.txt', system_qm_params_file='host_qm_params.txt', reparameterised_intermediate_system_xml_file='host_intermediate_reparameterised.xml', system_xml_non_bonded_file='host_xml_non_bonded.txt', system_xml_non_bonded_reparams_file='host_xml_non_bonded_reparams.txt', reparameterised_system_xml_file='host_reparameterised.xml', non_reparameterised_system_xml_file='host.xml', prmtop_system_non_params='host_non_params.prmtop', inpcrd_system_non_params='host_non_params.inpcrd', prmtop_system_params='host_params.prmtop', inpcrd_system_params='host_params.inpcrd', load_topology='openmm')[source]

Methods

__init__([system_pdb, system_sdf, charge, ...])

analyze_diff_energies()

Compares the energies of the ligand obtained from the non-parameterized and the parameterized force field files.

save_amber_params()

Saves amber generated topology files for the ligand.

serialize_system()

write_reparameterised_system_xml()

Writes a reparameterised XML force field file for the ligand.

write_system_params()

Saves the parameters obtained from the QM log files in a text file.