openforcefield.utils.structure.generateProteinStructure¶

openforcefield.utils.structure.generateProteinStructure(proteinpdb, protein_forcefield='amber99sbildn.xml', solvent_forcefield='tip3p.xml')[source]¶

Given an OpenMM PDBFile, create the OpenMM System of the protein using OpenMM’s ForceField and then generate the parametrized ParmEd Structure of the protein.

Parameters:	proteinpdb : simtk.openmm.app.PDBFile object, Loaded PDBFile object of the protein. protein_forcefield : xml file, default=’amber99sbildn.xml’ Forcefield parameters for protein solvent_forcefield : xml file, default=’tip3p.xml’ Forcefield parameters for solvent
Returns:	solv_structure : parmed.structure.Structure The parameterized Structure of the protein with solvent molecules. (No ligand).