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No output with docking full protocol

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No output with docking full protocol

Hello everyone,

I'm trying to dock a protein with an ssDNA using the full protocol flags :

-s protein_ssDNA.pdb
-partners A_H
-database /home/useradmin/Rosetta/main/database/


But, I obtain the message error :

protocols.docking.DockingProtocol:  Scoretype: interchain_contact score: 12, cutoff: 9.99
protocols.docking.DockingProtocol:  Scoretype: interchain_vdw score: 0, cutoff: 1
protocols.jd2.FileSystemJobDistributor: Too many retries (max_retry_job = 10)
protocols.jd2.JobDistributor: HBsAg_Aptamer_0001_0001 reported failure and will retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 11 jobs attempted in 68 seconds

Can anyone know the solution to overpass this problem and realize the docking protocol protein/ssDNA ?

Best regards

Post Situation: 
Mon, 2016-05-30 02:16

Answered in

Briefly, you can't, as RosettaDock low resolution doesn't recognize protein/nucleic acid interactions. You can do full atom refinement, but no global searching.

There's work in progress to change this, but nothing in a usable state, as of yet.

Fri, 2016-06-17 10:24