I am using rosetta docking_protocol.linuxiccrelease @flags > docking.log for initial protein docking. 10000 initial pose(only backbone) were generated by this. Then I clustered top200 pose by cluster.linuxiccrelease @flags >& cluster.log &
The best scoring one from the largest cluster were submitted for rosetta refinement(add sidechain and hydrogens) :relax.linuxgccrelease @flags > log
I try to use the refined protein complex for high resolution docking, but it doesn't work. All the pose generated by high resolution protein-protein docking are the same with my initial refined protein complex.
Does anybody have any suggestions?
Thank you very much