Thanks very much.
It was a great constraint setting instead of binding site, I think. I will try it later.
An additional question was about how I could construct a rmsd verse energy score plot to evaluate these abundant candidate structures, as docking does(complex with lowest energy was set to input)? Is it feasible for floppytail?
Initially, I would like to just copy the procedures in prepack options of Rosettadocking. However, I saw that there was no native structure input option. I also tried score_jd2.linuxgccrelease, but a hint said that no weight file was rendered.
If possible, could you give me any hint? Thanks a lot.