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Error when using RabD with a nanobody.

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Error when using RabD with a nanobody.

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/


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 .


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! 


error.log14.21 KB
cdr_instructions.txt396 bytes
RabD_flag.txt850 bytes
Post Situation: 
Mon, 2018-12-17 04:40

I'm facing the same issue.


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



Mon, 2018-12-17 09:17

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




Mon, 2018-12-17 11:35

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.




Fri, 2019-01-25 09:54

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. 

Mon, 2019-01-28 08:46

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!  



Mon, 2018-12-17 11:34