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 B) 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?