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.

See our manual

PDBFixer can be installed with conda or mamba.

conda install -c conda-forge pdbfixer

Alternatively you can install from source, as described in the manual.