Error when using RabD with a nanobody.

Member Site › Forums › Rosetta 3 › Rosetta 3 – General › Error when using RabD with a nanobody.

Viewing 2 reply threads
  • Author
    Posts
    • December 17, 2018 at 12:40 pm #3061
      Anonymous

        Hi Everyone,

        Recently, I am using RabD to design my nanobodies, But I can not perform it smoothly:

         

        >>>Error returns:

        ERROR] Exception caught by JobDistributor for job complex.1_0001

         

        File: src/protocols/antibody/AntibodyInfo.cc:1117

         

        L1 start resnum not found in pose: 24 L

        Please check pdb is renumbered properly and the passed -numbering_scheme option matches the PDB.

        This could also mean missing density in the cdr loop.  Loop modeling applications can be used to fill missing residues

         

        Program did not found L chain, which is not in a nanobody. And  my structure is already renumber in AHO using PyIgClassfiy.py .

         

        However, rosetta had already record the antibody type as Camelid Antibody

        ////////////////////////////////////////////////////////////////////////////////

        ///                          Rosetta Antibody Info                           ///

        ///                                                                          ///

        ///             Antibody Type:  Camelid Antibody

        ///             Light Chain Type:  unknown

        /// Predict H3 Cterminus Base:  NEUTRAL

        ///

        My Rosetta version is 2018.33.60351_bundle / 2017.52.59948_bundle all not working.

         

        Attached is my run files and error.log…

         

        who can help me to see what happening?

        Thank you very much! 

         

      • December 17, 2018 at 5:17 pm #14544
        Anonymous

          I’m facing the same issue.

           

          I hope there’s some kind of troubleshootting for this.

           

          Danilo.

          • December 17, 2018 at 7:35 pm #14546
            Anonymous

              I’ve fixed the bug in a branch and added a new test.  The fix will be available in the next weekly release.

               

              Cheers,

              -Jared

            • January 25, 2019 at 5:54 pm #14569
              Anonymous

                Hi Jared,

                 

                Any idea when the next weekly release will be released? The last one that I can find was released on December 2nd, 2018.

                 

                Best,

                Danilo.

              • January 28, 2019 at 4:46 pm #14570
                Anonymous

                  I looked into it, and unfortunately, the weekly releases are held up at the moment.  I’ll post here when the next one is released.  Should be in the next week or two. 

              • December 17, 2018 at 7:34 pm #14545
                Anonymous

                  I’ve identified the bug and fixed it in a branch, including a new test for this.  The fix will be included in the next weekly release!  Thanks for reporting it!  

                   

                  -Jared

              • Author
                Posts
              Viewing 2 reply threads
              • You must be logged in to reply to this topic.