Homology modeling

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    • August 17, 2009 at 8:04 pm #337
      eprocko
      Participant

        Hello,

        Is there good documentation or a tutorial on how to use Rosetta 3.0 to construct a homology model based on a user-input template?

        Documentation is not clear (or is absent).

        Any help is most welcomed. I am able to generate a backbone model, but unable to generate a fullatom model.

        thanks, Mike

      • August 17, 2009 at 8:23 pm #4152
        eprocko
        Participant

          The error I am getting when running the following:

          /usr/local/rosetta3.0/bin/loopmodel.gcc.i686
          -database /usr/local/rosetta3.0/rosetta3_database
          -nstruct 2
          -in:file:fullatom
          -loops::input_pdb template.pdb
          -loops::loop_file loops.file
          -loops::frag_sizes 9 3
          -loops::frag_files aaquery09_05.200_v1_3 aaquery03_05.200_v1_3
          -out:file:fullatom

          is:

          “ERROR: Could not find disulfide partner for residue”

        • August 18, 2009 at 5:49 pm #4153
          Anonymous

            Do you have disulfides in your protein?

            As of 3.0, the “detect_disulfides” flag defaults to true, you can try turning this to false, especially if you do not have disulfides.

            There is a flag “fix_disulf” which lets you specify where you know the disulfides are – I’ve never used it and have no idea if it’s compatible with loop modeling.

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