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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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Run pdb2pqr as python library #338

Open dargen3 opened 1 year ago

dargen3 commented 1 year ago

Hello,

I'd like to thank you for pdb2pqr. It's a great tool! I would like to ask for your help. I am using pdb2pqr30 to protonate the structure using bash command:

pdb2pqr30 --log-level DEBUG --noopt --titration-state-method propka --with-ph <ph> --pdb-output <pdb_output> <pdb_input> <pqr_file> Could you please guide me how to execute this command using the python API described by https://pdb2pqr.readthedocs.io/en/latest/api/index.html? I've tried it for hours with no results. You can also add this as an example on the API web page. I think enough users would appreciate it.

Regards, Ondrej

sobolevnrm commented 1 year ago

Can you please share the code you've written so far and the problems you have encountered?