I am relatively new to PyRosetta and am having difficulties getting flexpep_docking to work. I have tried both FlexPepDockingAbInitio and FlexPepDockingLowRes, and when I try to apply either one to my pose I don't get an error message, but it simply doesn't do anything to my pose. I've invested a lot of time trying to set it up different ways, but nothing I've tried so far has worked. When I try to apply AbInitio to my pose, it just outputs a series of temperatures, and when I try to apply LowRes it doesn't output anything. I have a known region on the protein that I want to dock the peptide to, so the entire AbInitio protocol isn't necessary. Does anyone have a flexpep_docking script that they know works, and if so is there a way to restrict the search to a small region?