From Mantis: 0000008: Explicit hydrogens and documentation for molfile_to_params.py

[everyday847]

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.