Docking seems to not parse the -nstruct flag

[Anonymous]

Hello all,

I am new to Rosetta, and I am trying to get RosettaDock to work.

For the sake of simplicity, I just want to do a refinement dock, with no constraints (though I will eventually want to graduate to incorporating these).

The command I run, a modification on the example commands in Chaudhury et al. 2011:
(I did prepacking before this, with seemingly no issue.
Also, I removed the -database flag, it was causing errors and Rosetta programs seems to work without it.)

name=protein
nstruct=10 # Just for testing
chains1=AB
chains2=CD

${ROSETTA_BIN}/docking_protocol.linuxgccrelease
-overwrite
-ignore_zero_occupancy false
-s ${name}_prepack.pdb
–nstruct ${nstruct}
-partners ${chains1}_${chains2}
-docking_local_refine
-ex1 -ex2aro -use_input_sc -unboundrot ${name}_dock.pdb > dock.log

produces the following error:

unbound energy: -764.326
protocols.docking.DockingProtocol.metrics: bound energy: -768.901
protocols.docking.DockingProtocol.metrics: interaction energy: -4.57554
protocols.docking.DockingProtocol.metrics: rb_jump: 1
protocols.jd2.JobDistributor: protein_prepack_0001 reported success in 86 seconds
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB –nstruct
core.import_pose.import_pose: PDB File:–nstruct not found!
Error: ERROR: Exception caught by JobDistributor while trying to get pose from job ‘–nstruct_0001’
Error:

[ERROR] EXCN_utility_exit has been thrown from: src/core/import_pose/import_pose.cc line: 214
ERROR: Cannot open PDB file “–nstruct”

Error: Treating failure as bad input; canceling similar jobs
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: –nstruct_0001
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB 10
core.import_pose.import_pose: PDB File:10 not found!
Error: ERROR: Exception caught by JobDistributor while trying to get pose from job ’10_0001′
Error:

[ERROR] EXCN_utility_exit has been thrown from: src/core/import_pose/import_pose.cc line: 214
ERROR: Cannot open PDB file “10”

Error: Treating failure as bad input; canceling similar jobs
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: 10_0001
protocols.jd2.JobDistributor: no more batches to process…
protocols.jd2.JobDistributor: 3 jobs considered, 3 jobs attempted in 109 seconds
caught exception 2 jobs failed; check output for error messages

This was weird, almost as if the -s flag was reading into the -nstruct flag. So, I tried switching the -nstruct and -s line, which produced a different weird error:
ERROR: ERROR: Unused “free” argument specified: –nstruct

Seems I can get it to run, provided I don’t include the -nstruct flag. But, then, it looks like it just does one cycle, hard to tell. It finishes very quickly and only produces one structure.

Seems like the program isn’t parsing the -nstruct flag, or I’m doing something else wrong, but I’m not sure what to do, because this is what the online documentation says to do. If you have any advice, I would appreciate it, thanks!

Best regards,
David J. Rosenman
Postdoctoral Researcher at University of Delaware

P.S. I may as well ask another question while I am here:
In a general, non-refinement dock, is there a way to control how many decoys are generated at the coarse level, and how many are generated at the fine level? I only see the nstruct flag, which I presume would affect the coarse docking, but not the fine docking without the -docking_local_refine flag.

[Anonymous]

You have too many (two) dashes in -nstruct.  You want only one dash.

To your second question: no, not really.  This is a feature planned for a future Job Distributor in Rosetta, which may eventually percolate back to old docking protocols.

[Anonymous]

ARGH, now I feel silly. That makes sense. The PDF to text when I copied the Chaudhury example must have interpreted hyphen instead of dash. My editor is fixed font, and I didn’t see the difference. But here, it shows up. 

Thanks for your help!

[Author]

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