I am trying to perform a protein-protein docking simmulation between two proteins, A and B. Both protein has bound ligand, I know Rosetta cannot run with both ligand, So in a run, I remove ligand. But, I would like to give constrain 5A residue of surrounding the ligand. I already checked the constrain tutorial but I found that atom pair only give CA of amino acid. Atom pair wouldn't work for me. My question is I want to give full amino acid as a constraint. Totally will be around 10 amino acid as a constraint in each protein. Could you please help me with this? Please let me how can configuration and constraints file.
Thanks in advanced.