FAQ

Known Limitations

Can I add my own charge and radius parameters to PDB2PQR?

Can PDB2PQR output create a PQR file using forcefield-specific residue and atom names?

Does the input PDB file need to be in a specific format?

How do I add my own functionality to PDB2PQR?

How is PDB2PQR licensed?

I already know the protonation state of a residue. How can I make PDB2PQR aware of it?

What causes the following warning: “WARNING: PDB2PQR was unable to assign charges to the following atoms”?

What force fields or parameter sets are available?

What is a PQR file?

What is PEOE_PB?

What is PROPKA?

What platforms, compilers, and architectures are compatible with PDB2PQR?

What types of residues can PDB2PQR recognize?

Why are chain IDs not included in the output by default?