Residue Topology Recognition

Another useful functionality of pmlbeta is residue topology recognition. For actual work with molecular models an accurate designation of various portions of the molecule (“residues”, e.g. amino-acids or other building blocks) and atom naming is often required. While the models constructed by betafab are labeled according to the nomenclature of the CHARMM force field, re-labeling for a different molecular mechanics force field or labeling an unlabeled molecule (e.g. obtained from crystallography or NMR experiments) is sometimes needed. This package has the following methods:

  • Given the N-terminal nitrogen and the C-terminal carbon atoms, command renumber_peptide_chain finds and marks the residues in a peptide chain (either α or β).
  • Command residue_topology_candidates finds matching building block topologies from a GROMACS residue topology database file for each residue in the molecule using graph isomorphishm.
  • Command assign_residue_topology assigns atom properties (name, residue name, partial charge) from a corresponding building block topology in a GROMACS topology database
  • The functionality of the above two commands is implemented in a user-friendly graphical tool accessible from the menu.