Symmetric local protein docking

[Anonymous]

Hi.
I installed Rosetta3.1 and I’m trying to use it for local docking of protein complexes witn Cn symmetry.
The program docking_protocol.linuxgccrelease is running and produces the results but it prints out a warning:
“core.scoring.SymmetricScoreFunction: Warning!!! Using a symmetric score function on a non-symmetric pose”

I’ll be happy to know what am I doing wrong…

Here are my steps:
1) I have a model of a trimer that I want to refine.
I deleted one of the monomers and saved the remaining 2 monomers (chains A and in a pdb file.
2) I ran prepacking by:
docking_protocol.linuxgccrelease -database rosetta_database -s res.AB.pdb -docking:dock_ppk
3) I prepared the symmetry definition file by:
make_symmdef_file.pl -m NCS -a A -i B -r 12.0 -p res.AB.pdb > ! symm.AB.def
4) I ran rosettaDock by:
docking_protocol.linuxgccrelease -database rosetta_database -s res.AB_0001.pdb -nstruct 10 -ex1 -ex2
-out:file:fullatom -out:file:o res -symmetry:symmetry_definition symm.AB.def -symmetry:initialize_rigid_body_dofs
-symmetry:perturb_rigid_body_dofs 3 8

Is this process correct?
Why do I get a warning?

Thanks!
Efrat.

[Anonymous]

Here’s a reply from Ben Stranges:

“I guess the documentation isn’t very clear on this. They are using the wrong PDB as input for the docking step, everything up until that point looks good.
After you run the make_symmdef_file.pl script there are several outputs. The one that the symmetry code needs as input is *_INPUT.pdb. It is a monomer which is used in conjunction with the symmetry code to make the dimer.
In this case the cmd line should be:

docking_protocol.linuxgccrelease -database rosetta_database -s res.AB_0001_INPUT.pdb -nstruct 10 -ex1 -ex2
-out:file:fullatom -out:file:o res -symmetry:symmetry_definition symm.AB.def -symmetry:initialize_rigid_body_dofs
-symmetry:perturb_rigid_body_dofs 3 8″

[Anonymous]

Thanks a lot for the quick reply.
I tried your suggestion and got a different error when running docking_protocol.linuxgccrelease.

Here is the error:
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 126 -1
protocols.docking.DockingProtocol:
ERROR: cutpoint
ERROR:: Exit from: src/protocols/docking/DockingProtocol.cc line: 284

My steps were:
1) I have a model of a trimer that I want to refine.
I deleted one of the monomers and saved the remaining 2 monomers (chains A and in a pdb file.
2) I ran prepacking by:
docking_protocol.linuxgccrelease -database rosetta_database -s res.AB.pdb -docking:dock_ppk
3) I prepared the symmetry definition file by:
make_symmdef_file.pl -m NCS -a A -i B -r 12.0 -p res.AB_0001.pdb > ! symm.AB.def
4) I ran rosettaDock by:
docking_protocol.linuxgccrelease -database rosetta_database -s res.AB_0001_INPUT.pdb -nstruct 1 -ex1 -ex2 -out:file:fullatom -out:file:o res -symmetry:symmetry_definition symm.AB.def -symmetry:initialize_rigid_body_dofs -symmetry:perturb_rigid_body_dofs 3 8

Thanks,
Efrat.

[Anonymous]

OK, I got a different reply from Ingemar (the author of this code):

“The symmetric docking protocol has not yet been publicly released in Rosetta 3. The docking_protocol app handles only heterodimeric docking, hence the issues you are seeing. The great thing though is that symmetric docking will be part of the next release of Rosetta (3.2), which is imminent. Until then you have to live with the version in Rosetta 2.*”

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