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SNUGDOCK

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SNUGDOCK
#1

Hello,

I tried running snugdock on ROSIE. The run finished and when I downloaded the output files from the server, I got this messge in the output.json file:

{
  "cpu_usage": 0.9324999999999994, 
  "docked_proteins": [], 
  "essential": [
    "trigger-00000.prepack_trigger/proteins_prepacked.pdb", 
    "trigger-00001.snug_dock_trigger/score.sf"
  ], 
  "log": "\nCould not find essential file trigger-00000.prepack_trigger/proteins_prepacked.pdb in DB!\n", 
  "prepak.pdb": "output/trigger-00000.prepack_trigger/proteins_prepacked.pdb", 
  "score.sf": "output/trigger-00001.snug_dock_trigger/score.sf", 
  "status": 0
}

 

However, I do have a proteins.prepacked.pdb file in the  output\trigger-00000.prepack_trigger directory.

The job number is 52615. Please help.

 

Thanks,

Harsh

Category: 
Post Situation: 
Tue, 2018-10-09 23:58
harsh

Error in json file is a bit missleading in this case. The real error could be seen here: http://rosie.graylab.jhu.edu/fs/52615/output/logs/.hpc.snug_dock.output.0.log i am posting relevant part of the log below:

 

[ERROR] Exception caught by JobDistributor for job proteins_0004
H1 start resnum for North definition not found in pose: 23 H  
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 

 

 

Tue, 2018-10-16 15:52
Sergey