Dear Open Babel support team,
I tried to protonate a ligand from a PDB file and save a protonated PDB
that keeps the atom label (e.g.: C2A) and residue name.
The PDB openbabel exported just leaves element type (e.g.: C) but not the
original atom label (e.g.: C2A). And the residue name was changed to 'UNL'
but not the original '4CO'.
Detail:
I tried using both the command line:
obabel XXX.pdb -o pdb -O XXX2.pdb --p 7.0
and also python API:
mol = next(pybel.readfile('pdb', path))
mol.OBMol.AddHydrogens(False, True, ph)
mol.write('pdb', out_path, overwrite=True)
This is an original pdb line:
ATOM 2 C2A 4CO 371 66.999 58.130 14.636 1.00 0.00
This is one after openbabel:
HETATM 2 C UNL 1 66.999 58.130 14.636 1.00 0.00 C
Is there any way I can keep the atom label at least?
All the Best,
Qianzhen
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