Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › protein docking failed
- This topic has 6 replies, 5 voices, and was last updated 11 years, 4 months ago by Anonymous.
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November 8, 2012 at 10:59 am #1455Anonymous
hello:
I am docking a two proteins: one is with 900 aa the the left is 200 aa. here is my protocol:
/home/albert/install/rosetta3.4/rosetta_source/bin/docking_protocol.linuxgccrelease
-database /home/albert/install/rosetta3.4/rosetta_database
-nstruct $nstruct
-s ../input.pdb
-docking:docking_local_refine true
-docking:dock_pert 3 8
-docking:spin true
-docking:dock_min true
-ex1
-ex2
-out:path:pdb ./
-out:suffix $i
-out:file:fullatom
-out:pdbthe job failed with messages:
ERROR: total_residue() != 0
ERROR:: Exit from: src/core/pose/Pose.cc line: 1042thank you very much
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November 8, 2012 at 3:14 pm #8055Anonymous
A) It may be useful to post the PDB, as usually problems like this are flaws with the PDB input.
Of the flags:
-docking:docking_local_refine true
-docking:dock_pert 3 8
-docking:spin true
-docking:dock_min true
You can only pick one of those, as they are all mutually exclusive. What style of docking do you actually want? -
November 8, 2012 at 4:02 pm #8063Anonymous
thanks for reply.
I am going to do high resolution protein/protein docking to refine the local position. -
June 9, 2013 at 4:37 am #8879Anonymous
Hi
I have same question.
After High-res docking only,I am going to do High-res docking minimization.Here is my protocol:
-s 1brs_0001_0001_0001_0001.pdb-ex1
-ex2aro
-use_input_sc
-no_filters
-docking_local_refine
-dock_min
-mute core.util.prof
-out:overwrite
-out:pdb
-mute core.io.database
the job failed with messages:
ERROR: total_residue() != 0
ERROR:: Exit from: src/core/pose/Pose.cc line: 1042
Here is my PDB input files.
Thank you very much! -
November 8, 2012 at 4:04 pm #8064Anonymous
Of those four flags, you want only -docking:docking_local_refine true.
I still need more information, like the PDB input, to diagnose the main error. If you can’t post it for some reason, check that the occupancy column is all nonzero and that there are exactly two chains in the protein.
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June 10, 2013 at 3:16 pm #8881Anonymous
Strange. Can you try this on Rosetta3.5 to see if you get the same error?
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June 10, 2013 at 9:28 pm #8885Anonymous
After some debugging, it looks like a MonteCarlo object isn’t getting initialized properly, so it gives back an empty pose when it rejects a move.
The best way to fix it would be to go to rosetta_source/src/protocols/docking/DockMinMover.cc line 142 and uncomment (remove the first two slashes) the line:
// mc_->reset(pose); // JQX: I think it is not necessary
and then recompile. (The call does turn out to be necessary.)
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