You are here

Docking Local Refine Not Moving Input

2 posts / 0 new
Last post
Docking Local Refine Not Moving Input


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"/>


        <InitializeFromCommandline name="cmdTask"/>
        <RestrictToRepacking name="repackOnly"/>


        <PackRotamersMover name="repack" scorefxn="t14" task_operations="cmdTask,repackOnly"/>
      <DockingProtocol name="docker" docking_local_refine="1" partners="LH_A"/>


        <Add mover="docker"/>



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.

1vfb_start.pdb467.67 KB
Post Situation: 
Sat, 2017-10-21 08:26

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.

Mon, 2017-11-20 13:27