conf/split_protocol/flex_ddG-mutation_step.xml

<ROSETTASCRIPTS>
  <SCOREFXNS>
    <ScoreFunction name="fa_fxn" weights="talaris2014"/>
    <ScoreFunction name="fa_fxn_cst" weights="talaris2014">
      <Reweight scoretype="atom_pair_constraint" weight="1.0"/>
      <Set fa_max_dis="9.0"/>
    </ScoreFunction>
  </SCOREFXNS>

  <TASKOPERATIONS>
    <ReadResfile name="res_mutate" filename="%%mutate_resfile_relpath%%"/>
  </TASKOPERATIONS>

  <RESIDUE_SELECTORS>
    <Task name="resselector" fixed="0" packable="0" designable="1" task_operations="res_mutate"/>
    <Neighborhood name="bubble_helper" selector="resselector" distance="%%neighbor_distance%%" include_focus_in_subset="true"/>
    <NativeSelector name="bubble" residue_selector="bubble_helper" />
    <PrimarySequenceNeighborhood name="bubble_adjacent" selector="bubble" lower="1" upper="1"/>
    <StoredResidueSubset name="restore_neighbor_shell" subset_name="neighbor_shell"/>
    <Not name="everythingelse" selector="restore_neighbor_shell"/>
  </RESIDUE_SELECTORS>
  <TASKOPERATIONS>
    <OperateOnResidueSubset name="repackonly" selector="restore_neighbor_shell">
      <RestrictToRepackingRLT/>
    </OperateOnResidueSubset>
    <OperateOnResidueSubset name="norepack" selector="everythingelse">
      <PreventRepackingRLT/>
    </OperateOnResidueSubset>
    <UseMultiCoolAnnealer name="multicool" states="6"/>
    <ExtraChiCutoff name="extrachizero" extrachi_cutoff="0"/>
    <InitializeFromCommandline name="commandline_init"/>
    <RestrictToRepacking name="restrict_to_repacking"/>
  </TASKOPERATIONS>

  <MOVERS>
    <AddConstraintsToCurrentConformationMover name="addcst" use_distance_cst="1" coord_dev="0.5" min_seq_sep="0" max_distance="9" CA_only="1" bound_width="0.0" cst_weight="0.0"/>
    <ClearConstraintsMover name="clearcst"/>
    <MinMover name="minimize" scorefxn="fa_fxn_cst" chi="1" bb="1" type="lbfgs_armijo_nonmonotone" tolerance="%%min_tolerance%%" max_iter="%%min_max_iter%%" abs_score_convergence_threshold="%%min_abs_score_convergence_threshold%%"/>

    <PackRotamersMover name="mutate" scorefxn="fa_fxn" task_operations="commandline_init,res_mutate,norepack,multicool"/>

    <ReportToDB name="dbreport" batch_description="interface_ddG" database_name="ddG.db3">
      <ResidueFeatures/>
      <ScoreTypeFeatures/>
      <ScoreFunctionFeatures scorefxn="fa_fxn"/>
      <StructureScoresFeatures scorefxn="fa_fxn"/>
      <HBondFeatures scorefxn="fa_fxn"/>
      <InterfaceFeatures scorefxn="fa_fxn" pack_together="false"/>
    </ReportToDB>

    <ReportToDB name="structreport" batch_description="interface_ddG_struct" database_name="struct.db3">
      <PoseConformationFeatures/>
      <PdbDataFeatures/>
      <JobDataFeatures/>
      <ResidueFeatures/>
      <PoseCommentsFeatures/>
      <ProteinResidueConformationFeatures/>
      <ResidueConformationFeatures/>
      <RotamerFeatures/>
      <ResidueBurialFeatures/>
    </ReportToDB>

    <SavePoseMover name="save_wt_bound_pose" restore_pose="0" reference_name="wt_bound_pose"/>
    <LoadPDB name="load_backrub_pdb" filename="%%backrub_pdb_path%%"/>

    <InterfaceDdGMover name="int_ddG_mover" wt_ref_savepose_mover="save_wt_bound_pose" chain_name="%%chainstomove%%" db_reporter="dbreport" scorefxn="fa_fxn"/>

    <ScoreMover name="apply_score" scorefxn="fa_fxn_cst" verbose="0"/>
    <StoreResidueSubset name="neighbor_shell_storer" subset_name="neighbor_shell" residue_selector="bubble_adjacent" />

  </MOVERS>
  <APPLY_TO_POSE>
  </APPLY_TO_POSE>
  <PROTOCOLS>
    <Add mover_name="save_wt_bound_pose"/>

    <Add mover_name="load_backrub_pdb"/>
    <Add mover_name="neighbor_shell_storer"/>

    <Add mover_name="addcst"/>
    <Add mover_name="apply_score"/>
    <Add mover_name="clearcst"/>
    <Add mover_name="mutate"/>

    <Add mover_name="addcst"/>
    <Add mover_name="minimize"/>
    <Add mover_name="clearcst"/>
    <Add mover_name="structreport"/>

    <Add mover_name="int_ddG_mover"/>

    <Add mover_name="dbreport"/>
  </PROTOCOLS>
  <OUTPUT />
</ROSETTASCRIPTS>