Hi
I've been wondering why docking protocol moves protein which i dont want to be moved
so in my case, I have a complex PDB file with chain A, B, and C.
A is a small protein, and B and C is neighboured together, and C is the receptor
What i want to do is docking A to C, while B and C is not moved or designed.
so i made a xml script like below:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="ref2015" weights="ref2015.wts" />
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Chain name="scaffold" chains="A"/>
<Index name="C" resnums="602C-741C"/>
<Index name="B" resnums="1B-601B"/>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<InitializeFromCommandline name="ifcl"/>
<RestrictToRepacking name="rtr" />
<RestrictToInterfaceVector name="rtiv" chain1_num="1,2" chain2_num="3" CB_dist_cutoff="10.0" nearby_atom_cutoff="5.5" vector_angle_cutoff="75" vector_dist_cutoff="9.0" />
<OperateOnResidueSubset name="B" selector="B"><PreventRepackingRLT />
</OperateOnResidueSubset>
<OperateOnResidueSubset name="C" selector="C"><PreventRepackingRLT />
</OperateOnResidueSubset>
</TASKOPERATIONS>
<FILTERS>
</FILTERS>
<MOVERS>
<FastDesign name="FastDesign" scorefxn="ref2015" task_operations="ifcl,B,C,rtiv"/>
<SaveAndRetrieveSidechains name="srsc" allsc="0" />
<DockingProtocol name="docking_high" docking_score_high="ref2015" docking_local_refine="1" task_operations="ifcl,B,C" partners="C_A"/>
</MOVERS>
<APPLY_TO_POSE>
</APPLY_TO_POSE>
<PROTOCOLS>
<Add mover="FastDesign" />
#Add mover="docking_low"/>
#Add mover="srsc" />
<Add mover="docking_high"/>
#Add mover="dock_high" />
#Add mover="minimize_interface" />
</PROTOCOLS>
</ROSETTASCRIPTS>
The reason why i used docking protocol is just because i want to get I_sc value, because so far I know, using docking mover doesnt give I_sc value..
After running this xml, i see my chain B and C also moved and seems repacked.
I just dont want repacking or moving B and C, but i dont know what will be the best way to improve my xml script
Could you please give me any advice to handle this problem?????
Thanks