Symmetric local protein docking

Member Site Forums Rosetta++ Rosetta++ – General Symmetric local protein docking

Viewing 1 reply thread
  • Author
    • #741


        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 ,
        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,

      • #4834

          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?

      Viewing 1 reply thread
      • You must be logged in to reply to this topic.