I'm docking a short peptide fragment (2 residues) into a small binding pocket that only accommodates one residue. Since the binding pocket is hydrophobic and binds hydrophobic peptides, I expected that Rosetta would give a poor score to peptide mutant such as lys, his, arg. But it scores these quite well. If I don't dock, but just score after using the fixed backbone protocol to make the mutants, the results are quite good. However, sometimes there is a lot of clashing, and the peptide's side chain is pointed out of the binding pocket. Is there any way to restrict the type of docking to be less aggressive, perhaps less backbone movement?