SnugDock: chain_id H represents more than one chain

This topic has 1 reply, 2 voices, and was last updated 6 years, 7 months ago by Anonymous.

Viewing 1 reply thread

Author

Posts
- May 2, 2018 at 11:24 am #2907
  Anonymous
  Hi,
  
  I want to use snugdock in Rosie to model the binding structure between an antibody and an antigen. This is my input: http://rosie.rosettacommons.org/fs/46862/input/proteins.pdb
  
  I get the following error message:
```
[ERROR] Exception caught by JobDistributor for job proteins_0066chain_id H represents more than one chain!#
```
  The job status is ‘finished’, but I don’t see any output structures or graphs. When using docking2 instead, it works normally. This is the job: http://rosie.rosettacommons.org/snug_dock/viewjob/46862
  
  How do I fix this error? I consulted already this forum and the documentation but didn’t find any help.
- May 2, 2018 at 1:38 pm #14216
  Anonymous
  Rosetta’s SnugDock application expects three chains: “the light chain coming first, then the heavy chain, and finally the antigen.” Your PDB file has many breaks in the heavy chain, and each break contains a “TER” (chain termination) record. Rosetta is seeing that as multiple chains.
  
  It should work if you remove all the lines beginning with TER, except the one at the end of chain H, (between the antibody and the antigen). The one between the heavy and light chains can probably be left in, too. Then Rosetta will see the heavy chain as a single chain, and should not give that error.
Author

Posts

Viewing 1 reply thread

You must be logged in to reply to this topic.