SNUGDOCK

[Anonymous]

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  outputtrigger-00000.prepack_trigger directory.

The job number is 52615. Please help.

 

Thanks,

Harsh

[Anonymous]

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 

 

 

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