Symmetric local protein docking

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    • January 17, 2011 at 12:52 pm #741
      Anonymous

        Hi.

        I installed Rosetta2.3 and I’m trying to use it for local docking of protein complexes witn Cn symmetry.
        For my first try, I’m trying to refine the solved trimer with PDB code 1QU9

        I tryied to follow the instructions in http://www.rosettacommons.org/guide/Symmetrical%20Docking ,
        and these were my steps:
        1. I downloaded the file 1qu9.pdb
        2. prepaking:
        rosetta.release aa 1qu9 _ -dock -s 1qu9 -prepack_full -quiet -ex1 -ex2aro_only
        3. symmetric local docking:
        rosetta.release aa 1qu9 _ -dock -pose -docking_pose_symmetry -symm_type cn -pose_symm_n_monomer 3 -docking_pose_symm_full -dock_mcm -ex1 -ex2aro_only -dock_rtmin -s 1qu9.ppk.pdb

        However, during the run I got an error of memory corruption:
        …
        Symmetry docking with cn symmetry
        Jump #1 from 56 to 253
        Jump #2 from 182 to 254
        Jump #3 from 253 to 254
        *** glibc detected *** rosetta.release: malloc(): memory corruption: 0x0a8e4df0 ***

        Please help me understand the problem.

        Best regards,
        Efrat.

      • January 18, 2011 at 3:44 pm #4834
        Anonymous

          It sounds like there’s a memory bug – either accessing a deleted pointer, or pointing off the end of an array, or something.

          I assume it’s reproducible?

          The jumps listed look a little odd to me, but that knowing it’s weird doesn’t really help solve the problem. How many residues are supposed to be in the protein, and should it be evenly divided into thirds?

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