We want to compute partial charges for proteins in PDB format. We use the Gasteiger algorithm from rdkit.Chem but some files cause errors. Maybe you'll recommend another implementation or another algorithm?
Example error for PDB ID 1a0a:
ERROR: No Gasteiger Partial Charge parameters for Element: P Mode:
The reason: there are hard-coded partial charges that are used as initial parameterization (https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/PartialCharges/GasteigerParams.cpp). The problem is that the hard-coded partial charges are associated with a pair of the form (atom_name, mode) where mode is the Hybridization of the atom. In the file 1a0a, the problem is that the P atom in question has hybridization SP3D, while in the hardcoded parameters there is a partial charge only for the pair (P, SP3), but not for (P, SP3D).
I know nothing about PDB files (sorry about that) but would recommend you change your username since your current username suggests you are affiliated to this forum.