I want to relax a protein with a ligand in a specific position using the simple "relax.linuxgccrelease" program. However, I found that if the atom names (third column at the PDB) are not as expected, the output "relaxed" PDB shows a weird ligand (it looks more like an insect than a molecule), regardless if the ligand is already parameterized in Rosetta (Sorbitol [SOR] in this case). Once the atom names are fixed, the relaxed structures make sense.
I managed to transform my original molecule with OpenBabel and to edit the different fields with PyMol scripting, but finding the correct naming of the atoms is not trivial (I have to do it by hand and I need to test hundred of molecules with my protein).
Does someone know a way of doing this automatically? (see my files below)