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jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
GNU Lesser General Public License v2.1
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pKa informed protonation? #149

Closed akranc1 closed 2 years ago

akranc1 commented 2 years ago

Is there currently any native way in propka to use the calculated pKas to inform the protonation of amino acids in imported pdb files? I essentially need to be able to add all backbone hydrogens, as well as appropriate titratable hydrogens to be added.

sobolevnrm commented 2 years ago

You can use PDB2PQR to add hydrogens based on the protonation states assigned by PROPKA.