qmmmrebind.parameterize.GuestAmberXMLAmber

class qmmmrebind.parameterize.GuestAmberXMLAmber(charge=0, num_charge_atoms='', charge_atom_1='', index_charge_atom_1='', system_pdb='guest_init_II.pdb', system_mol2='guest.mol2', system_in='guest.in', system_frcmod='guest.frcmod', prmtop_system='guest.prmtop', inpcrd_system='guest.inpcrd', system_leap='guest.leap', system_xml='guest_init.xml', system_smi='guest.smi', system_sdf='guest.sdf', system_init_sdf='guest_init.sdf', index_charge_atom_2=' ', charge_atom_2=' ', charge_parameter_file='guest_qm_surround_charges.txt', system_qm_pdb='guest_init_II.pdb', bond_parameter_file='guest_bonds.txt', angle_parameter_file='guest_angles.txt', system_qm_params_file='guest_qm_params.txt', reparameterised_intermediate_system_xml_file='guest_intermediate_reparameterised.xml', system_xml_non_bonded_file='guest_xml_non_bonded.txt', system_xml_non_bonded_reparams_file='guest_xml_non_bonded_reparams.txt', reparameterised_system_xml_file='guest_reparameterised.xml', non_reparameterised_system_xml_file='guest_init.xml', prmtop_system_non_params='guest_non_params.prmtop', inpcrd_system_non_params='guest_non_params.inpcrd', prmtop_system_params='guest_params.prmtop', inpcrd_system_params='guest_params.inpcrd', load_topology='openmm')

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

This class contain methods to generate a template XML force field through openforcefield. XML template generation can be obtained through different file formats such as PDB, SDF, and SMI. Methods support charged ligands as well. Re-parameterized XML force field files are then generated from the template files. Different energy components such as the 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

• charge (int) – Charge of the ligand.

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

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

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

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

• system_mol2 (str, optional) – Ligand 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 ligand PDB.

• inpcrd_system (str, optional) – Coordinate file obtained from the ligand 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) – Serialized XML force field file of the ligand.

• system_smi (str, optional) – Ligand SMILES format file.

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

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

• index_charge_atom_2 (int, optional) – Index of the second charged atom of the ligand.

• charge_atom_2 (int, optional) – Charge on the second charged atom of the ligand.

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

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

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

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

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

• reparameterised_intermediate_system_xml_file (str, optional) – XML foce 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 ligand.

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

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

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

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

__init__(charge=0, num_charge_atoms='', charge_atom_1='', index_charge_atom_1='', system_pdb='guest_init_II.pdb', system_mol2='guest.mol2', system_in='guest.in', system_frcmod='guest.frcmod', prmtop_system='guest.prmtop', inpcrd_system='guest.inpcrd', system_leap='guest.leap', system_xml='guest_init.xml', system_smi='guest.smi', system_sdf='guest.sdf', system_init_sdf='guest_init.sdf', index_charge_atom_2=' ', charge_atom_2=' ', charge_parameter_file='guest_qm_surround_charges.txt', system_qm_pdb='guest_init_II.pdb', bond_parameter_file='guest_bonds.txt', angle_parameter_file='guest_angles.txt', system_qm_params_file='guest_qm_params.txt', reparameterised_intermediate_system_xml_file='guest_intermediate_reparameterised.xml', system_xml_non_bonded_file='guest_xml_non_bonded.txt', system_xml_non_bonded_reparams_file='guest_xml_non_bonded_reparams.txt', reparameterised_system_xml_file='guest_reparameterised.xml', non_reparameterised_system_xml_file='guest_init.xml', prmtop_system_non_params='guest_non_params.prmtop', inpcrd_system_non_params='guest_non_params.inpcrd', prmtop_system_params='guest_params.prmtop', inpcrd_system_params='guest_params.inpcrd', load_topology='openmm')

Methods

__init__([charge, num_charge_atoms, ...])
analyze_diff_energies()	Compares the energies of the ligand obtained from the non-parameterized and the parameterized force field files.
generate_xml_antechamber()	Generates an XML forcefield file from the PDB file through antechamber.
generate_xml_from_charged_pdb_sdf()	Generates an XML forcefield file for a singly charged ligand molecule from the SDF file through openforcefield.
generate_xml_from_doubly_charged_pdb_sdf()	Generates an XML forcefield file for a singly charged ligand molecule from the SDF file through openforcefield.
generate_xml_from_pdb_sdf()	Generates an XML forcefield file from the SDF file through openforcefield.
generate_xml_from_pdb_smi()	Generates an XML forcefield file from the SMILES file through openforcefield.
save_amber_params()	Saves amber generated topology files for the ligand.
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.