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Anonymous
There are two ways to incorporate Zinc into the PDB file.
1)edit the line in the PDB file with Zinc by changing ‘HETATM’ to ‘ATOM’ and the atom name to “Zn2p”. You can see the parameters for Zinc in /minirosetta_database/chemical/atom_type_sets/fa_standard/atom_properties.txt
2) use the molfile_to_params.py script as you tried to use. In the ligand_docking script download on the website (http://www.pyrosetta.org/scripts.html), you can find the rosetta_py folder which contains the necessary library to run the script. See the readme in that zip file for more information on using the script.