pdbfixer

PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation for simulating them. It can automatically fix the following problems: Add missing heavy atoms. Add missing hydrogen atoms. Build missing loops. Convert non-standard residues to their standard equivalents. Select a single position for atoms with multiple alternate positions listed. Delete unwanted chains from the model. Delete unwanted heterogens. Build a water box for explicit solvent simulations. (Summary from the program web page.)

The official web page: https://github.com/openmm/pdbfixer

Typical usage

$ module add pdbfixer
$ pdbfixer