I can run rosetta docking protocol on my pdb file and there is no problem when I define partners as "MN_A". However, the same doesn't work on pyrosetta demo code of docking. I tried to solve this in several different ways by changing the docking jump value or etc but nothing acheived! Output models are still wrong in the format of M_NA. How can I fix this?
I'm trying to use this docking protocol as part of my workflow so I need to know if this is a solved problem or I have to use only one chains for each partners in pyrosetta. Please also let me know if I can define the movable jumps in the fold tree.
Thanks a lot for all your help in advance,