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

PDBFixer fixes problems in PDB files

Adding hydrogens to molecular models

macromolecular crystallography library and utilities

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

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