I am doing unbound docking and i believe I have enough biological info to locate the binding interface and rough orientation. Doing the docking manually (or with the low res protocol) suggests that there's some conformational change in the interface that I would like to model. I'm guessing this is not something that I can accomplish with the old docking_protocol commandline app. I did see a flexible_bb_docking option but that appears to be undocumented? Maybe I can do this via the ensembles options?
I understand that everyone does docking using rosetta scripts nowadays but I don't have any experience with that and don't really see any published docking scripts to start with. There was a question asked a couple years ago but I don't see the attached script there any more : https://www.rosettacommons.org/node/3531