The molfile_to_params.py file is only used to create a residue type description (params file) of a single ligand. You would _not_ use it to convert a full enzyme-ligand complex.
Instead, you’d process just the respresentative structure of your ligand (as a mol file) through the molfile_to_params.py script. Your enzyme-ligand complex would instead be entered directly into Rosetta as a PDB formatted file. The only trick is to make sure that the three letter code of your ligand in the PDB file matches the three letter code that’s specified in the params file.
If you have your complex as a mol file, I’d recommend going back to the program which generated the mol file of the complex and asking it to generate a PDB file instead. (There are ways to convert a mol file to a PDB file, but they tend not to work well in the abstract. It’s better to go back to the program which originally generated the mol file and get it to do the conversion.)
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