Docking Local Refine Not Moving Input

[Anonymous]

Hi,

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:

<ROSETTASCRIPTS>

    <SCOREFXNS>

        <ScoreFunction name=”t14″ weights=”talaris2014″/>

    </SCOREFXNS>

    <RESIDUE_SELECTORS>

    </RESIDUE_SELECTORS>

    <TASKOPERATIONS>

        <InitializeFromCommandline name=”cmdTask”/>

        <RestrictToRepacking name=”repackOnly”/>

    </TASKOPERATIONS>

    <FILTERS>

    </FILTERS>

    <MOVERS>

        <PackRotamersMover name=”repack” scorefxn=”t14″ task_operations=”cmdTask,repackOnly”/>

      <DockingProtocol name=”docker” docking_local_refine=”1″ partners=”LH_A”/>

    </MOVERS>

    <APPLY_TO_POSE>

    </APPLY_TO_POSE>

    <PROTOCOLS>

        <Add mover=”docker”/>

    </PROTOCOLS>

</ROSETTASCRIPTS>

 

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.

[Anonymous]

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.

[Author]

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