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protein location change during Docking protocol

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protein location change during Docking protocol


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:

          <ScoreFunction name="ref2015" weights="ref2015.wts" />
          <Chain name="scaffold" chains="A"/>
          <Index name="C" resnums="602C-741C"/>
          <Index name="B" resnums="1B-601B"/>
          <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 name="C" selector="C"><PreventRepackingRLT />
          <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"/>

          <Add mover="FastDesign" />
          #Add mover="docking_low"/>
          #Add mover="srsc" />
          <Add mover="docking_high"/>
          #Add mover="dock_high" />
          #Add mover="minimize_interface" />



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?????



Post Situation: 
Tue, 2022-03-29 19:53