We have seen PDB files that do not adhere to atom typing. There may be ways to work around this, but it would be helpful if RINRUS can diagnose certain problems with PDB files and formatting by giving warnings in the stdout and/or driver log file.
See: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/83PROD_QChem.pdb
where side chain proton types were either inappropriately renamed or used an ancient/non-standard atom typing scheme
Most side chain "HXn" protons where n = 2 & 3 are incorrectly typed to have n = 1 & 2. So "HB1" in an ASP for example is an atom type not recognized by res_atoms.py and presumably ignored in the RIN.
We have seen PDB files that do not adhere to atom typing. There may be ways to work around this, but it would be helpful if RINRUS can diagnose certain problems with PDB files and formatting by giving warnings in the stdout and/or driver log file.
See: https://github.com/gorangiud/MolSSI_COVID-19_hub-base/blob/main/83PROD_QChem.pdb where side chain proton types were either inappropriately renamed or used an ancient/non-standard atom typing scheme Most side chain "HXn" protons where n = 2 & 3 are incorrectly typed to have n = 1 & 2. So "HB1" in an ASP for example is an atom type not recognized by res_atoms.py and presumably ignored in the RIN.