Error : seqpos <= size()

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    • October 6, 2014 at 12:20 am #2026
      Anonymous

        Dear Rossetta Users,

        when I run Flexpepdock protocol, the error is : “ERROR: seqpos <= size()
        ERROR:: Exit from: src/core/conformation/Conformation.hh line: 289:.

        Can someone here explain why this happenned?
        I attach the input file below.

        Best regards
        Phan Vy

      • October 6, 2014 at 7:21 pm #10387
        Anonymous

          Can you attach your command line with any flags that you used? Does the result change at all if you remove the zinc ion?

        • October 6, 2014 at 11:06 pm #10396
          Anonymous

            Dear everyday847,
            I removed Zinc, but the error still return (same above)

            This is the flag for running prepack before running Flexpepdock protocol

            s starting.pdb
            -database /home/tuongvy/SW/rosetta3.4/rosetta_database

            -flexpep_prepack
            -ex1
            -ex2aro

            I got starting structure from Molecular Dynamics simulation.
            Thank a lot and best regard

            Phan Vy

          • October 6, 2014 at 11:46 pm #10399
            Anonymous

              Your “occupancy” column in the PDB is zero, which means Rosetta will ignore those atoms by default. (Leading to an empty structure.)

              Use the option “-ignore_zero_occupancy false” to override this behavior and use all the atom coordinates specified in the PDB.

            • October 7, 2014 at 4:18 am #10402
              Anonymous

                rmoretti!
                Thank a lot for your help. It work now

                Phan Vy

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