xyzVector error in Enzyme design

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    • January 5, 2016 at 5:46 pm #2361
      Anonymous

        Dear all,

        I’m using rosetta’s enzyme design app from build “rosetta_bin_linux_2015.31.58019_bundle”. The problem is that the calculation stops very frequently with the following error:

        …

        core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for LG1

        core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for LG1

        core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for LG1

        core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for LG1

        Error: Must call shutdown() when finished using job distributor!

        caught exception Cannot normalize xyzVector of length() zero

         

        I read somewhere that it may be a coding problem, but I have no idea and did not find any info on this error.

        Anyone knows what’s happening?

         

        Cordially,

        Armenio Barbosa

      • January 5, 2016 at 5:58 pm #11391
        Anonymous

          Could you provide your ligand params file, constraints file and input PDB? (You can PM me if it’s something you’d prefer not to post publically.)

          This is likely something that will be difficult to debug without a hands-on example to play around with.

        • June 10, 2016 at 2:28 am #11617
          Anonymous

            I also have this problem, but only on one cluster. The same job with the same constraints and params file works elsewhere.

            [ERROR] Exception caught by JobDistributor for job CP7PXN_ETS_0005 Cannot normalize xyzVector of length() zero

          • June 17, 2016 at 5:36 pm #11665
            Anonymous

              If you’re only getting the error occasionally, I wouldn’t be too worried about it. Sometimes it happens that the random numbers are such that you get a zero length vector.

              I’d only be concerned if you consistently get the error with different random number seeds on different Rosetta runs.

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