I'm trying to generate small perturbations of a protein-protein complex, and so I've tred to use the docking local refine mover. I tested out the mover on a simple test system (an antibody-antigen complex) but when I look at my output structures, I see no difference relative to my input structure. Am I using the correct mover? (again, I only want small perturbations). Am I not seeing differences because my input structure is already at an energy minimum? I see no difference, even in sidechains - I would have expected to at least see some sidechains repacked relative to input.
The xml I'm using is:
<ScoreFunction name="t14" weights="talaris2014"/>
<PackRotamersMover name="repack" scorefxn="t14" task_operations="cmdTask,repackOnly"/>
<DockingProtocol name="docker" docking_local_refine="1" partners="LH_A"/>
I'm calling the script using:
~/rosetta/bin/rosetta_scripts.linuxgccrelease -s 1vfb_start.pdb -ex1 -ex2 -parser:protocol dock.xml -nstruct 5
My input pdb is attached. It is an X-ray structure that I have processed using rosetta (constrained relax).
Thanks in advance.
Just wanted to follow up to see if anyone has a suggestion for a good way to make small perturbations to a protein-protein complex, starting from the native structure. I've been using docking_local_refine (see above), but that doesn't seem to work.