molfile_to_params script error

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    • July 8, 2015 at 4:22 am #2234
      Anonymous

        Greetings, I’ve been following the “design with non-canonical aa” demo (located on demos/public/design_with_ncaa) in order to set parameters for a custom residue “CYM”, which is a deprotonated cysteine. Yet I got stuck in the last step namely, when I try to convert my modified .mol file to params using:

        “python molfile_to_params_polymer.py cym.mol –clobber –polymer –no-pdb –name CYM -k cym.kin”

        it returns:

        “Traceback (most recent call last):
        File “../../Rosetta/demos/public/design_with_ncaa/scripts/python/apps/publi//molfile_to_params_polymer.py”, line 1995, in
        sys.exit(main(sys.argv[1:]))
        File “../../Rosetta/demos/public/design_with_ncaa/scripts/python/apps/public/molfile_to_params_polymer.py”, line 1953, in main
        polymer_assign_pdb_like_atom_names_to_sidechain( m.atoms, m.bonds, options.peptoid )
        File “../../Rosetta/demos/public/design_with_ncaa/scripts/python/apps/public/molfile_to_params_polymer.py”, line 1697, in polymer_assign_pdb_like_atom_names_to_sidechain
        a.pdb_greek_dist = greek_alphabet[all_all_dist[ca_index]]
        TypeError: list indices must be integers, not float”

        But if I skip the –polymer flag, it actually converts my .mol file, but it is defined as ligand and is not recognized by Rosetta.
        The same error was already posted ( https://www.rosettacommons.org/node/3763 ), but the source of the problem seems unrelated to my case, as CYM is a Cys-like residue without obvious connection issues that could cause the failure.
        I would really appreciate any help you can give me to solve this error.

        The .mol file being used as imput is attached as a .txt file.

        Thanks

      • July 14, 2015 at 9:59 pm #11100
        Anonymous

          It looks like your issue is your POLY_UPPER and POLY_IGNORE lines. Your POLY_UPPER is pointing to the hydrogen, rather than the nitrogen. Also, you’re missing some atoms (carbonyl oxygen 12 and the amide hydrogen 18) in the POLY_IGNORE line. – That’s where the error is coming from. It’s trying to find the through-bond distance from oxygen 12 to the rest of the non-ignored atoms, and is coming up with “1e+100” which is representing an invalid distance (as it’s not connected once the POLY_LOWER 11 is removed from consideration).

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