flexpep docking problem

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    • April 19, 2011 at 12:15 am #877
      Anonymous

        Dear All:
        I am very new to the peptide flexible docking. When I use the locally installed rosetta 3.2.1 to perform a peptide docking. I got the error as :

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

        The command line is :
        FlexPepDocking.linuxgccrelease -database /usr/local/src/rosetta_database/ -s renum.pdb -flexpep_prepack > flex.log

        I also attached the pdb file and log file.

        Hope you can help me out! thank you so much!!

        Best wishes,

      • April 19, 2011 at 10:36 am #5453
        Anonymous

          I am having the same problem. The line refrred to in the error talks about the occupancy entries in the pdb file, but it doesn’t help when I set them all to 1.00.
          command: /home/rosetta-3.2/rosetta_source/bin/FlexPepDocking.linuxgccrelease -s input.pdb -database /home/rosetta-3.2/rosetta_database/ -flexpep_prepack -ex1 -ex2aro
          An idea of what the problem is would be appreciated.
          Dave

          EDIT: OK it works so long as the native structure is included in the command

        • April 20, 2011 at 1:32 am #5456
          Anonymous

            Dear pardave:
            Could you kindly show me the command line and the input file(pdbs, native structure, flags etc.). So I can find the problems in my case. Thank you so much!!

          • April 20, 2011 at 1:41 am #5457
            Anonymous

              Dear All:
              by following the comment of pardave, I add the -native renum.pdb in my command. It goes well and finished the calculation successfully. So in summary:
              1, use some script to renumber your protein, best way is start from residue number 1. ( I don’t know this is the real issue. But If I use the discontinued residue numbers, the flexpep_docking program crashed with the segment fault error.)
              2, use the command including the -native *.pdb ( can be same as the -s *.pdb)

              Hoping this is useful to you.

              Best wishes,

            • April 20, 2011 at 9:21 am #5458
              Anonymous

                Dear Michael and Dave,

                The problem is definitely on the account of a missing “-native” structure. As repeatedly noted in the documentation the -native flag is required by FlexPepDock. It is used for RMSD calculations, as michael mentioned you can input the starting structure (same one you use for ‘-s’) or a different reference structure (like the actual solution, or a different model, etc…)

                Regrading discontinuous numbering, this should pose no problem, Michael, if you can reproduce the scenario please send us the cmd-line and PDB and we’ll check it out.

                Thanks,
                Nir.

              • April 21, 2011 at 5:06 am #5473
                Anonymous

                  Dear Nir:
                  Yes, you are right. I check the structure I used before and found some occupancy column is 0.00. So rosetta recognize as no atoms in residue. Then it printed out many missing atoms error, and finally it crashed. So in general, discontinuous numbers of residue DID NOT have problems.
                  Thanks all the discussions.

                  Best wishes,

                  Michael

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