SnugDock: chain_id H represents more than one chain

[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.

[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.

 

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