qmmmrebind.parameterize.RunOpenMMSims

class qmmmrebind.parameterize.RunOpenMMSims(system_prmtop, system_inpcrd, system_pdb, system_xml, system_output='sim_output.pdb', sim_steps=1000)[source]

A class used to run the OpenMM simulation on any specified system.

This class contain methods to run a MD simulation to confirm the proper structure of the reparameterized forcefield files.

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Variables

  • system_prmtop (str) – Topology file of the system (receptor, ligand or receptor - ligand complex)

  • system_inpcrd (str) – Coordinate file of the system (receptor, ligand or receptor - ligand complex)

  • system_pdb (str) – PDB file of the system to run MD simulation (receptor, ligand or receptor - ligand complex).

  • system_xml (str) – Serialised XML file for the system.

  • 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.

__init__(system_prmtop, system_inpcrd, system_pdb, system_xml, system_output='sim_output.pdb', sim_steps=1000)[source]

Methods

__init__(system_prmtop, system_inpcrd, ...)

run_openmm_prmtop_inpcrd()

Runs OpenMM MD simulation with prmtop and inpcrd file.

run_openmm_prmtop_pdb()

Runs OpenMM MD simulation with prmtop and PDB file.