I am using the model-ligand.py script. My protein in multi-chained, do I have to make changes in the header of the aligenment file? I have put (.) sign at the end of the alignment file and also made option env.io.hetatm is set to True but when I am running the model-ligand.py, a error is coming that there is a mismatch between the alignment and PDB.

Subarna Thakur