FlexPepDocking.mpi.linuxgccrelease bails out ERROR: total_residue() != 0 ERROR:: Exit from: src/core/pose/Pose.cc line: 1369

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    • February 3, 2011 at 11:24 am #764
      Anonymous

        When I tries to use FlexPepDocking it bails out ERROR: total_residue() != 0. Though I have been able to use the same pdb file with the web server. It appears that FlexPepDocking generate a pose that do not contain any residues and that the assert statement in Pose.cc bails out due to this reason. Is there anything wrong with my pdb file, I have also tried to include a co-factor which is parameterized. This error appear but with and witouth any co-factor.

        FlexPepDockingPoseMetrics: (1) Isc: -8.11514
        FlexPepDockingPoseMetrics: (1) Total BSA is: 659.381
        FlexPepDockingPoseMetrics: (1) Interface HB #: 1
        FlexPepDockingPoseMetrics: (1) Interface Unsat polar groups: 3
        FlexPepDockingPoseMetrics: (1) 155 bsa: 43.0976 HB: 0 unsat: 0
        FlexPepDockingPoseMetrics: (1) 156 bsa: 39.4691 HB: 0 unsat: 0
        FlexPepDockingPoseMetrics: (1) 157 bsa: 37.8193 HB: 0 unsat: 1
        FlexPepDockingPoseMetrics: (1) 158 bsa: 99.3032 HB: 0 unsat: 0
        FlexPepDockingPoseMetrics: (1) 159 bsa: 88.2471 HB: 1 unsat: 1

        ERROR: total_residue() != 0
        ERROR:: Exit from: src/core/pose/Pose.cc line: 1369

        MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
        with errorcode 911.

        NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
        You may or may not see output from other processes, depending on
        exactly when Open MPI kills them.

        Knut J

      • February 3, 2011 at 3:36 pm #4931
        Anonymous

          Can you post your input PDB? Does it have all nonzero occupancies in the occupancies column?

        • February 6, 2011 at 4:33 pm #4937
          Anonymous

            The input pdb is produce using Rosetta docking_protocol.mpi.linuxgccrelease. Is there any error in the pdb. I am sure that there are none nonzero occupancies. I have also parm files for the heatatom in the file.
            I solved this error by adding -native pdb

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