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Anonymous
From the params file, I see you’re modeling the chromophore as an independent ligand, rather than a non-canonical amino acid. Therefore, you’re likely to get phenomenally high VDW repulsive energies where the atoms of the chromophore and the atoms of the protein backbone make covalent bonds with each other (because Rosetta isn’t seeing them as covalent bonds).
BTW, I notice you don’t have any hydrogens on your chromphore. Rosetta is parametrized off of full atom (with hydrogen) structures. The results you get aren’t going to be as good if you protonate the mol2 file prior to molfile_to_params, especially when you’re missing polar hydrogens, (This doesn’t have anything to do with your fa_rep issue, though.)