read parameters of metal ions

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    • July 19, 2011 at 3:38 pm #981
      Anonymous

        Hi!

        How can I read parameters of several metal ions, solvent molecules or ligands?

        When I try to run this:
        from rosetta import *
        init()
        params_list=Vector1()
        res_set = generate_nonstandard_residue_set(params_list)

        I get the following error:
        …
        In [4]: res_set = generate_nonstandard_residue_set(params_list)
        core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 7533 residue types

        ERROR: Residue names must be unique!
        ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 358

        RuntimeError Traceback (most recent call last)

        /data/mcm/henricsn/sysmolab/results/2011-07_LmPYK/ in ()

        /scratch/mcm/henricsn/lib/PyRosetta/rosetta/__init__.pyc in generate_nonstandard_residue_set(params_list)
        206 res_set.read_files(params_list, ChemicalManager.get_instance().atom_type_set(“fa_standard”),
        207 ChemicalManager.get_instance().mm_atom_type_set(“fa_standard”),
        –> 208 ChemicalManager.get_instance().orbital_type_set(“fa_standard”),
        209 )
        210 return res_set

        RuntimeError: unidentifiable C++ exception

        The paramfiles MG.params SO4.params K.params are in the same directory (attachment).
        Thanks for your help.

        Stefan

      • July 19, 2011 at 4:32 pm #5877
        Anonymous

          Well, as it says, residue names must be unique. One of your added ones is clashing with an existing one, or you’re managing to add them twice.

          I would guess it’s magnesium, given that that’s already in the default residue type set. My second guess would be that it’s a K-potassium versus K-lysine conflict.

        • July 21, 2011 at 9:14 am #5884
          Anonymous

            The problem of reading metal ions was coming from the spacing in the PDB file. The same problem was already posted in http://www.rosettacommons.org/content/some-application-troubles-when-using-resfile-flag

            Here is a sample script and a test pdbfile with correct spacing:

            from rosetta import *
            init()
            params_list=Vector1()
            res_set = generate_nonstandard_residue_set(params_list)
            p=Pose()
            pose_from_pdb(p, "test.pdb")

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