antibody – sequence position requested was 0

Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › antibody – sequence position requested was 0

Viewing 1 reply thread
  • Author
    Posts
    • September 27, 2021 at 7:26 pm #3844
      Anonymous

        Hi,

        I am trying to do some antibody structure prediction. During the grafting step for the sequence I am working with, it seems to get through making 4 models, but then crashes with the error message: 

        [FILE]: src/core/conformation/Conformation.hh

        [LINE]: 509

        [START_MESSAGE]

        [ ERROR ] UtilityExitException

        ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

        Anyone have any idea what is going wrong here? 

         

        Thank you! :) 

      • September 27, 2021 at 9:22 pm #16023
        Anonymous

          Hi. I don’t have any information on exactly why this happens. It appears to be a bug of some form in the template database. Most importantly, I recently experienced this and know how to bypass this error to complete the modeling!

          Since four models were generated successfully, the bug is in one of the templates for the fifth model. The critical flag you need here is “-exclude_pdbs <4-letter-pdbid>”. For me, I gathered from the log file that it was the “frh” template. It could be different for your antibody. Identify which templates are used for model 5 in the report.txt or report.json files and exclude the problem template from consideration using the aforementioned option. For me, this allowed for the protocol to proceed. Unless this is a particularly rare template, there is most likely minimal harm in excluding any single template.

          I hope this helps!

      • Author
        Posts
      Viewing 1 reply thread
      • You must be logged in to reply to this topic.