I have docked two proteins and Now I am going to design the binding interface of one of them while fix everything in the other. I mean I want to do protein protein interaction design. which part of rosetta would be for this job?? is it fixbb?
I would use RosettaScripts. Your best bet is to find an example XML that does approximatly what you want and then adapt it to the specifics.
(Disclamer: I'm not doing one-sided protein interface design:)
the problem is Im new to work with rosetta and bioinformatic, so I dont know How I should find rosetta script and use it. I want to know is it really wrong choice to use fix bb for this purpose?
That's a problem. You'll have the best sucess if somebody locally can help you.
However just googling for "Rosetta interface protein design" gives a usefull second hit https://www.rosettacommons.org/demos/latest/public/rosetta_scripts_pp-interfaceredesign/README.
This should get you started.