PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

PDBFixer fixes problems in PDB files

Adding hydrogens to molecular models

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

macromolecular crystallography library and utilities

A dependency-free cross-platform swiss army knife for PDB files.

Reduce - tool for adding and correcting hydrogens in PDB files

Computational Crystallography Toolbox

Packmol - Initial configurations for molecular dynamics simulations