I did perturbative docking using both rosetta2.3 and rosetta3.1, which gave me very different score vs. rmsd results. The rosetta2.3 results showed slight funnel in score vs. rmsd relationship, while the rosetta3.1 gave me results with no such kind of tendency at all. Anyone having similar experience with the new edition?
Following is the flags and commands comparison in rosetta2.3 and rosetta3.1:
rosetta2.3: -dock -pose -dock_mcm -dock_rtmin -quiet -nstruct 5000 -fake_native -randomize1 -randomize2 -ex1 -ex2aro_only -unboundrot
rosetta3.1: -packing:ex1 -nstruct 5000 -docking:spin -docking:randomize1 -docking:randomize2 -docking_local_refine
I tried to make the rosetta3.1 flags consistent with rosetta2.3, but some of the flags could not be turned on. any suggestions on how to improve the rosetta3.1 results? Thanks a lot.