[Solved] Docking in metalloprotease (Zinc problem)

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    • January 21, 2010 at 12:04 am #392
      Anonymous

        Hi, I’m a recent user of PyRosetta and because of this I’m having some problems with it. I’m trying to dock some peptides in a metalloprotease, and I want to keep the zinc in the active site.
        I tried to use the script “molfile_to_params.py” as it’s in the manual, but the script can’t find the libraries.

        >>>Traceback (most recent call last):
        >>> File “./molfile_to_params.py”, line 25, in
        >>> from rosetta_py.io.mdl_molfile import *
        >>>ImportError: No module named rosetta_py.io.mdl_molfile

        I searched for similar libraries, but I didn’t find them.

        Could I solve this? Is there another method to load the zinc?

        Thanks

        José Geraldo de Carvalho Pereira
        Master Student of Molecular Biology – Bioinformatics
        University of Campinas, Brazil

      • February 4, 2010 at 3:09 am #4324
        Anonymous

          There are two ways to incorporate Zinc into the PDB file.

          1)edit the line in the PDB file with Zinc by changing ‘HETATM’ to ‘ATOM’ and the atom name to “Zn2p”. You can see the parameters for Zinc in /minirosetta_database/chemical/atom_type_sets/fa_standard/atom_properties.txt

          2) use the molfile_to_params.py script as you tried to use. In the ligand_docking script download on the website (http://www.pyrosetta.org/scripts.html), you can find the rosetta_py folder which contains the necessary library to run the script. See the readme in that zip file for more information on using the script.

        • February 4, 2010 at 6:13 pm #4335
          Anonymous

            Update:

            Sorry, #1 in the previous post was incorrect, the atom name should be “ZN”, not “Zn2p” (see /minirosetta_database/chemical/residue_type_sets/fa_standard/metal_ions/ZN.params)

            Also make sure that you make the Zn residue a separate chain, as it is not part of a polypeptide chain (for example, designate it chain ‘X’).

            Here’s an example of a Rosetta-friendly Zn in PDB format:

            ATOM 1598 ZN ZN X 400 13.611 16.296 24.802 1.00 26.91 ZN

          • February 7, 2010 at 3:05 am #4339
            Anonymous

              I’m having some trouble with the method #1, above.
              I still get the unrecognized aa error, but loading the ZN.params in my params list produces the “names must be unique” error. The line for Zn in the .pdb is just like the example (but different atom number, etc. of course).

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