protein docking failed

[Anonymous]

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:pdb

the job failed with messages:

ERROR: total_residue() != 0
ERROR:: Exit from: src/core/pose/Pose.cc line: 1042

thank you very much

[Anonymous]

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?

[Anonymous]

thanks for reply.
I am going to do high resolution protein/protein docking to refine the local position.

[Anonymous]

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!

[Anonymous]

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.

[Anonymous]

Strange. Can you try this on Rosetta3.5 to see if you get the same error?

[Anonymous]

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.)

[Author]

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