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:
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