No output with docking full protocol

This topic has 1 reply, 2 voices, and was last updated 8 years, 7 months ago by Anonymous.

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- May 30, 2016 at 9:16 am #2433
  Anonymous
  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/
  
  -ex1
  
  -ex2aro
  
  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
- June 17, 2016 at 5:24 pm #11664
  Anonymous
  Answered in https://www.rosettacommons.org/content/no-output-pdb-files-after-docking-protein-and-dnarna
  
  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.
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