Help with filtering (Rosetta scripts)

[Anonymous]

Hello

I’m running running a pilot ROSETTA script to get the GreedyOptMutation mover with the ddg filter to work. But I get this error message;

ERROR: ERROR: No acceptable mutations found. All possible mutations failed at least one filter!

Any ideas on how to get the filter to allow trajectories with mutations that improve ddG and increases affinity between the 2 proteins contained in the .pdb?

My .xml looks like this:

 

<ROSETTASCRIPTS>

   <SCOREFXNS>

       <ScoreFunction name=”r15″ weights=”ref2015″/>

   </SCOREFXNS>

   <RESIDUE_SELECTORS>

   </RESIDUE_SELECTORS>

   <TASKOPERATIONS>

              <ReadResfile name=”res_mutate” filename=”resfile.txt”/>   

   </TASKOPERATIONS>

   <FILTERS>

       <Ddg name=”ddgFilter” scorefxn=”r15″ repack=”1″ chain_num=”2″/>

   </FILTERS>

   <MOVERS>

       <MinMover name=”min_torsion” scorefxn=”r15″ chi=”true” bb=”true” cartesian=”F” /> 

       <GreedyOptMutationMover name=”gopt” task_operations=”res_mutate” filter=”ddgFilter” scorefxn=”r15″ relax_mover=”min_torsion” />

    </MOVERS>

   <APPLY_TO_POSE>

   </APPLY_TO_POSE>

   <PROTOCOLS>

       <Add mover=”gopt”/>

   </PROTOCOLS>

   <OUTPUT />

</ROSETTASCRIPTS>

 

The resfile looks like this:

NATRO 

start

77 – 88 A ALLAAxc 

51 – 56 A ALLAAxc 

23 – 30 A ALLAAxc

 

[Anonymous]

My recommendation would be to adjust the threshold on your filter. The Ddg filter has an implicit threshold of -15 REU. Any mutation which isn’t at least as good as this will be ignored by the GreedyOptMutation. Depending on what you native interface is like, this may be way to stringent. If you add the option `threshold=”0.0″` to the Ddg tag, you’ll only throw out those mutations which Rosetta thinks are actually worse in the bound form than the unbound form.

You may want to play around with this value, depending on what you’re looking for, but starting out with a value of 0.0 is a good way to see if the issue is really the filter threshold, or something else.

[Author]

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