Homology modeling

Member Site Forums Rosetta 3 Rosetta 3 – General Homology modeling

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    • #337


        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

      • #4152

          The error I am getting when running the following:

          -database /usr/local/rosetta3.0/rosetta3_database
          -nstruct 2
          -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


          “ERROR: Could not find disulfide partner for residue”

        • #4153

            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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