The documentation does not point out that the molfile which is the input to molfile_to_params.py must already contain explicit hydrogens. (Unlike standard PDB inputs to Rosetta, which can be provided as heavy-atom only.)
Not having hydrogens on the input molfile means that the energies and binding positions in fullatom mode with the thus-generated params file will not be correct.
The documentation does not point out that the molfile which is the input to molfile_to_params.py must already contain explicit hydrogens. (Unlike standard PDB inputs to Rosetta, which can be provided as heavy-atom only.)
Not having hydrogens on the input molfile means that the energies and binding positions in fullatom mode with the thus-generated params file will not be correct.