pdb2pqr binary package in Ubuntu Trusty i386

 PDB2PQR is a Python software package that automates many of the common
 tasks of preparing structures for continuum electrostatics calculations.
 It thus provides a platform-independent utility for converting protein files
 in PDB format to PQR format. These tasks include:
  * Adding a limited number of missing heavy atoms to biomolecular structures
  * Determining side-chain pKas
  * Placing missing hydrogens
  * Optimizing the protein for favorable hydrogen bonding
  * Assigning charge and radius parameters from a variety of force fields
 .
 This package also includes PropKa, a tool to modify the protonation state of
 protein structures in the Protein Data Bank (PDB) format to match a given pKa
 value. It can also be used to refine NMR structures, which often yield
 inaccurate pKa values for some residues.

Source package