pdb2pqr

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. (Summary from the program web page.)

The official web page: http://www.poissonboltzmann.org/pdb2pqr

Typical usage

$ module add pdb2pqr
$ pdb2pqr --ff=amber 1SS9.pdb 1SS9.pqr