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The question about FavorNativeResidue

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The question about FavorNativeResidue
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 I  read the paper Rosetta and the Design of Ligand Binding Sites doi:10.1007/978-1-4939-3569-7_4.

 

then try to use  EnzRepackMinimize  to design the protein.

But FavorNativeResidue was set as 0.5-3.0, the mutant position numbers are same and there are too many mutant positions.

However, I use the PackRotamersMover  by changing  FavorNativeResidue and can get different mutant position numbers.

How can I solve it? Thanks.

 

The design part  was set  as https://pubs.acs.org/doi/abs/10.1021/jacs.5b06622

      <MOVERS>

              <EnzRepackMinimize name="desmin" design="1" repack_only="0" scorefxn_minimize="myscore" scorefxn_repack="soft_rep" minimize_rb="1" minimize_sc="1" minimize_bb="0" cycles="1" minimize_lig="0" min_in_stages="0" backrub="0" task_operations="init,edto,resfile_design,limchi2,linmem_ig" />

              <EnzRepackMinimize name="fin_min" repack_only="0" design="0" scorefxn_minimize="myscore" scorefxn_repack="myscore" minimize_rb="1" minimize_sc="1" minimize_bb="1" cycles="1" task_operations="init,edto_repack,resfile_repack,limchi2,linmem_ig"/> 

              <EnzRepackMinimize name="fin_rpkmin" repack_only="1" design="0" scorefxn_minimize="myscore" scorefxn_repack="myscore" minimize_rb="1" minimize_sc="1" minimize_bb="0" cycles="1" task_operations="init,edto_repack,resfile_repack,limchi2,linmem_ig"/> 

              <GenericMonteCarlo name="multides" mover_name="desmin" filter_name="interfE" trials="4" sample_type="low" temperature="0.6" drift="1"/> 

              <FavorNativeResidue name="fnr" bonus="1.5"/> 

      </MOVERS>

 

      <PROTOCOLS>

              <Add mover_name="fnr"/>

              <Add mover_name="multides"/>

              <Add mover_name="fin_min"/>

              <Add mover_name="fin_rpkmin"/>

      </PROTOCOLS>

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Fri, 2019-04-12 20:02
asbelx