I am experiencing the same kind of problem with pose docking. I think I am using correct input with rosetta, but in the end, the backbone is unchanged all the time.
my input is :
rosetta.exe aa myprot 1 -s 1 myprot.ppk -dock -pose -dock_mcm -dock_rtmin -nstruct 10 -fake_native -dock_pert 0 0 0 -ex1 -ex2aro_only -unboundrot -use_score12
and I also tried to add : -pose_loops_file myprot.pose_loops
but nothing happend, except for a normal rigid backbone docking.
do you know what I am doing wrong ?