With the structure read in, a parametrization step is performed. A stored, general protein xml file contains bond, angle and torsion parameters, which have been generated specifically for compatibility with the QUBE force field and are available for all atoms in standard residues, including NME/ACE caps. This general xml is used to map parameters to the protein in question, using the now stored structure. As described above for the ligands, atomic charges and volumes are extracted from the ONETEP output file, symmetrized (if required), and used to calculate the Lennard-Jones parameters. QUBEKit is then used to write pdb and xml files for use with OpenMM. Since each atom in the protein is in a unique environment, and therefore has unique charge and Lennard-Jones parameters, each atom in QUBEKit-pro is assigned a unique type.