I am trying to perform a local protein docking. The two docking partners are 5 A away from the native complex. What would be te right command to dock these structures locally. I tried to set the -dock_pert flag to 0 0 0. This still resulted in large numbers of decoys that where rotated with more than 80 degrees and translated more than 10 A.
This is the command I used:
rosetta AA 0001 _ -dock -dock_mcm -dock_rtmin -dock_pert 0 0 0 -s 0001.pdb -nstruct 200