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Segmentation fault in generate.inp

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  • Katya Heldwein
    Hi all, When I run generate.inp script in CNS 1.21, I get the message Segmentation fault . The last lines in the output file are CNSsolve do
    Message 1 of 3 , Sep 8, 2008
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      Hi all,

      When I run generate.inp script in CNS 1.21, I get the message "Segmentation
      fault". The last lines in the output file are

      CNSsolve> do (vx=maxwell($bath)) (store1)
      SELRPN: 1 atoms have been selected out of 4273
      CNSsolve> do (vy=maxwell($bath)) (store1)
      SELRPN: 1 atoms have been selected out of 4273
      CNSsolve> do (vz=maxwell($bath)) (store1)
      SELRPN: 1 atoms have been selected out of 4273
      CNSsolve>
      CNSsolve> flags exclude vdw include impr end
      CNSsolve>
      CNSsolve> dynamics cartesian

      It looks like the problem may stem from missing C-terminal OXT atom in
      the input pdb file. Generate in CNS 1.1 used to build missing OXT
      atoms, but this does not happen in CNS 1.21, for some reason.

      Does anyone know how to get CNS to build OXT atoms with correct
      coordinates for C-terminal residues? Alternatively, is there another
      program that can do this?

      If I include arbitrary coordinates for OXT, generate script runs just
      fine, but now I get "Segmentation fault" error with any kind of
      torsion dynamics. This problem may be unrelated, though. For example,
      these are the last lines of the output file for composite_omit_map
      script:

      CNSsolve> if ( &anneal = true ) then
      NEXTCD: condition evaluated as true
      CNSsolve> if ( &md_type = "torsion" ) then
      NEXTCD: condition evaluated as true
      CNSsolve> dyna tors


      Thanks,

      Katya
    • Axel Brunger
      This sounds to me like a compiler problem on your linux computer. Please use the latest Intel ifort, Portland Group pgf95, or Gfortran compilers on linux. I
      Message 2 of 3 , Sep 9, 2008
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        This sounds to me like a compiler problem on your linux computer.  Please use the
        latest Intel ifort, Portland Group pgf95, or Gfortran compilers on linux.

        I highly recommend that you use one of the pre-compiled
        CNS installations for Mac OS-X from the CNS download site, 
        or for both linux and Mac OS-X by joining SBGrid.org. 

        Please let me know if this solves your problems.

        Best regards,
        Axel Brunger




        On Sep 8, 2008, at 1:26 PM, Katya Heldwein wrote:

        Hi all,

        When I run generate.inp script in CNS 1.21, I get the message "Segmentation
        fault". The last lines in the output file are

        CNSsolve> do (vx=maxwell( $bath)) (store1)
        SELRPN: 1 atoms have been selected out of 4273
        CNSsolve> do (vy=maxwell( $bath)) (store1)
        SELRPN: 1 atoms have been selected out of 4273
        CNSsolve> do (vz=maxwell( $bath)) (store1)
        SELRPN: 1 atoms have been selected out of 4273
        CNSsolve>
        CNSsolve> flags exclude vdw include impr end
        CNSsolve>
        CNSsolve> dynamics cartesian

        It looks like the problem may stem from missing C-terminal OXT atom in
        the input pdb file. Generate in CNS 1.1 used to build missing OXT
        atoms, but this does not happen in CNS 1.21, for some reason.

        Does anyone know how to get CNS to build OXT atoms with correct
        coordinates for C-terminal residues? Alternatively, is there another
        program that can do this?

        If I include arbitrary coordinates for OXT, generate script runs just
        fine, but now I get "Segmentation fault" error with any kind of
        torsion dynamics. This problem may be unrelated, though. For example,
        these are the last lines of the output file for composite_omit_ map
        script:

        CNSsolve> if ( &anneal = true ) then
        NEXTCD: condition evaluated as true
        CNSsolve> if ( &md_type = "torsion" ) then
        NEXTCD: condition evaluated as true
        CNSsolve> dyna tors

        Thanks,

        Katya


        Axel T. Brunger
        Investigator,  Howard Hughes Medical Institute
        Professor of Molecular and Cellular Physiology
        Stanford University

        Email:  brunger@...      
        Phone:  +1 650-736-1031
        Fax:    +1 650-745-1463






      • Axel Brunger
        One more thing: please make sure you set limit stacksize unlimited on your machine. The default stacksize is often too small, causing unpredictable
        Message 3 of 3 , Sep 9, 2008
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          One more thing: please make sure you set

          limit stacksize unlimited

          on your machine.  The default stacksize is often too small,
          causing unpredictable segmentation faults.

          Axel Brunger


          On Sep 8, 2008, at 1:26 PM, Katya Heldwein wrote:

          Hi all,

          When I run generate.inp script in CNS 1.21, I get the message "Segmentation
          fault". The last lines in the output file are

          CNSsolve> do (vx=maxwell( $bath)) (store1)
          SELRPN: 1 atoms have been selected out of 4273
          CNSsolve> do (vy=maxwell( $bath)) (store1)
          SELRPN: 1 atoms have been selected out of 4273
          CNSsolve> do (vz=maxwell( $bath)) (store1)
          SELRPN: 1 atoms have been selected out of 4273
          CNSsolve>
          CNSsolve> flags exclude vdw include impr end
          CNSsolve>
          CNSsolve> dynamics cartesian

          It looks like the problem may stem from missing C-terminal OXT atom in
          the input pdb file. Generate in CNS 1.1 used to build missing OXT
          atoms, but this does not happen in CNS 1.21, for some reason.

          Does anyone know how to get CNS to build OXT atoms with correct
          coordinates for C-terminal residues? Alternatively, is there another
          program that can do this?

          If I include arbitrary coordinates for OXT, generate script runs just
          fine, but now I get "Segmentation fault" error with any kind of
          torsion dynamics. This problem may be unrelated, though. For example,
          these are the last lines of the output file for composite_omit_ map
          script:

          CNSsolve> if ( &anneal = true ) then
          NEXTCD: condition evaluated as true
          CNSsolve> if ( &md_type = "torsion" ) then
          NEXTCD: condition evaluated as true
          CNSsolve> dyna tors

          Thanks,

          Katya


          Axel T. Brunger
          Investigator,  Howard Hughes Medical Institute
          Professor of Molecular and Cellular Physiology
          Stanford University

          Email:  brunger@...      
          Phone:  +1 650-736-1031
          Fax:    +1 650-745-1463






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