protein docking failed

Member Site Forums Rosetta 3 Rosetta 3 – Applications protein docking failed

Viewing 3 reply threads
  • Author
    Posts
    • #1455
      Anonymous

        hello:

        I am docking a two proteins: one is with 900 aa the the left is 200 aa. here is my protocol:

        /home/albert/install/rosetta3.4/rosetta_source/bin/docking_protocol.linuxgccrelease
        -database /home/albert/install/rosetta3.4/rosetta_database
        -nstruct $nstruct
        -s ../input.pdb
        -docking:docking_local_refine true
        -docking:dock_pert 3 8
        -docking:spin true
        -docking:dock_min true
        -ex1
        -ex2
        -out:path:pdb ./
        -out:suffix $i
        -out:file:fullatom
        -out:pdb

        the job failed with messages:

        ERROR: total_residue() != 0
        ERROR:: Exit from: src/core/pose/Pose.cc line: 1042

        thank you very much

      • #8055
        Anonymous

          A) It may be useful to post the PDB, as usually problems like this are flaws with the PDB input.

          B) Of the flags:
          -docking:docking_local_refine true
          -docking:dock_pert 3 8
          -docking:spin true
          -docking:dock_min true
          You can only pick one of those, as they are all mutually exclusive. What style of docking do you actually want?

        • #8063
          Anonymous

            thanks for reply.
            I am going to do high resolution protein/protein docking to refine the local position.

          • #8879
            Anonymous

              Hi
              I have same question.
              After High-res docking only,I am going to do High-res docking minimization.

              Here is my protocol:
              -s 1brs_0001_0001_0001_0001.pdb

              -ex1

              -ex2aro

              -use_input_sc

              -no_filters

              -docking_local_refine

              -dock_min

              -mute core.util.prof

              -out:overwrite

              -out:pdb

              -mute core.io.database

              the job failed with messages:

              ERROR: total_residue() != 0
              ERROR:: Exit from: src/core/pose/Pose.cc line: 1042
              Here is my PDB input files.
              Thank you very much!

            • #8064
              Anonymous

                Of those four flags, you want only -docking:docking_local_refine true.

                I still need more information, like the PDB input, to diagnose the main error. If you can’t post it for some reason, check that the occupancy column is all nonzero and that there are exactly two chains in the protein.

              • #8881
                Anonymous

                  Strange. Can you try this on Rosetta3.5 to see if you get the same error?

                • #8885
                  Anonymous

                    After some debugging, it looks like a MonteCarlo object isn’t getting initialized properly, so it gives back an empty pose when it rejects a move.

                    The best way to fix it would be to go to rosetta_source/src/protocols/docking/DockMinMover.cc line 142 and uncomment (remove the first two slashes) the line:

                    // mc_->reset(pose); // JQX: I think it is not necessary

                    and then recompile. (The call does turn out to be necessary.)

                Viewing 3 reply threads
                • You must be logged in to reply to this topic.