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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
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Add code warnings and documentation about the --keep-protons option being ignored #365

Closed dargen3 closed 1 year ago

dargen3 commented 1 year ago

Hello,

I'd like to report a potential bug. I protonated the structure with pdb2pqr30 --noopt --nodebump --keep-protons --pdb-output repaired_substructure.pdb substructure.pdb repaired_substructure.pqr Although I used --keep-protons flag hydrogen ATOM 223 HE2 HIS A 32 4.906 8.213 6.758 1.00 0.00 H is missing from the repaired_substructure.pdb file. I used pdb2pqr 3.6.1.

files.zip

sobolevnrm commented 1 year ago

Hello --

The --keep-protons flag is a PROPKA option, one of the libraries PDB2PQR uses. We provide access to the PROPKA options by popular request; however, this sometimes creates confusion when PDB2PQR overrides the PROPKA behavior. Since PDB2PQR optimizes and sometimes replaces hydrogens based on the predicted pKa and given pH, it ignores the --keep-protons keyword. I should update the documentation and/or the code to clarify this point. However, it only be a change to the documentation and will not follow the PROPKA behavior.

Thank you,

Nathan