from pdbfixer import PDBFixer
from openmm.app import PDBFile



# Load the PDB file

fixer = PDBFixer(filename='your_file.pdb')

# Find missing residues
fixer.findMissingResidues()

# Replace nonstandard residues
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()

# Find missing atoms and add them
fixer.findMissingAtoms()
fixer.addMissingAtoms()

# Write the fixed PDB file
PDBFile.writeFile(fixer.topology, fixer.positions, open('fixed_pdb.pdb', 'w'))