Assigning protonation states with PROPKA

[and-tos]

I'm new to PROPKA and from the documentation I found it's not clear to me if there's a way to add explicit proton atoms to a PDB file, or if the use is limited to the calculation of pKa values for titratable groups. I'd really appreciate any help pointing me in the right direction.

[sobolevnrm]

PDB2PQR uses PROPKA to add protons (and other missing atoms) to structures. It may be what you're looking for: https://github.com/Electrostatics/pdb2pqr