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ddG-backrub_Step2.xml
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ddG-backrub_Step2.xml
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<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="fa_talaris2014" weights="talaris2014"/>
<ScoreFunction name="fa_talaris2014_cst" weights="talaris2014">
<Reweight scoretype="atom_pair_constraint" weight="1.0"/>
<Set fa_max_dis="9.0"/>
</ScoreFunction>
</SCOREFXNS>
<!-- ### Only required input file (other than PDB) - mutation resfile ### -->
<!-- #### All residues must be set to be NATAA packable at top of resfile ### -->
<TASKOPERATIONS>
<ReadResfile name="res_inter" filename="%%inter_resfile_relpath%%"/>
<ReadResfile name="res_mutate" filename="%%mutate_resfile_relpath%%"/>
</TASKOPERATIONS>
<RESIDUE_SELECTORS>
<Task name="resselector" fixed="0" packable="0" designable="1" task_operations="res_inter"/>
<Neighborhood name="bubble" selector="resselector" distance="8.0"/>
<PrimarySequenceNeighborhood name="bubble_adjacent" selector="bubble" lower="1" upper="1"/>
<StoredResidueSubset name="restore_interface_shell" subset_name="interface_shell"/>
<Not name="everythingelse" selector="restore_interface_shell"/>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="repackonly" selector="restore_interface_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>
<FILTERS>
</FILTERS>
<MOVERS>
<StoreResidueSubset name="interface_shell_storer" subset_name="interface_shell" residue_selector="bubble_adjacent" />
<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_talaris2014_cst" chi="1" bb="1" type="lbfgs_armijo_nonmonotone" tolerance="0.000001" max_iter="%%max_minimization_iter%%" abs_score_convergence_threshold="%%abs_score_convergence_thresh%%"/>
<PackRotamersMover name="repack" scorefxn="fa_talaris2014" task_operations="commandline_init,repackonly,norepack,multicool"/>
<PackRotamersMover name="mutate" scorefxn="fa_talaris2014" task_operations="commandline_init,res_mutate,multicool"/>
<ReportToDB name="dbreport" batch_description="interface_ddG" database_name="ddG.db3">
<ScoreTypeFeatures/>
<ScoreFunctionFeatures scorefxn="fa_talaris2014"/>
<StructureScoresFeatures scorefxn="fa_talaris2014"/>
</ReportToDB>
<ReportToDB name="structreport" batch_description="interface_ddG_struct" database_name="struct.db3">
<PoseConformationFeatures/>
<PdbDataFeatures/>
<JobDataFeatures/>
<ResidueFeatures/>
<PoseCommentsFeatures/>
<ProteinResidueConformationFeatures/>
<ResidueConformationFeatures/>
</ReportToDB>
<SavePoseMover name="save_wt_bound_pose" restore_pose="0" reference_name="wt_bound_pose"/> <!--Somehow you should get this pose (wild-type pose) from the step 1 so you can calculate the ddG score using InterfaceDdGMover-->
<LoadPDB name="load_br_bound_pose" filename="%%br_pose_relpath%%"/>
<!--SavePoseMover name="save_backrub_pose" restore_pose="0" reference_name="backrubpdb"/-->
<!--SavePoseMover name="restore_backrub_pose" restore_pose="1" reference_name="backrubpdb"/-->
<InterfaceDdGMover name="int_ddG_mover" wt_ref_savepose_mover="save_wt_bound_pose" chain_name="%%chainstomove%%" db_reporter="dbreport" scorefxn="fa_talaris2014"/> <!--You need it in step 2 to calculate ddG score with respect to the wt pose (as reference) and mt pose (actual pose)-->
<ScoreMover name="apply_score" scorefxn="fa_talaris2014_cst" verbose="0"/>
<!-- This ParsedProtocol allows the ddG calculation to take place multiple times along the backrub trajectory, if desired -->
<ParsedProtocol name="finish_ddg_post_backrub">
<!--Add mover_name="save_backrub_pose"/-->
<!--Add mover_name="structreport"/-->
<!--Add mover_name="repack"/-->
<!--Add mover_name="addcst"/-->
<!--Add mover_name="minimize"/-->
<!--Add mover_name="clearcst"/-->
<!--Add mover_name="save_wt_bound_pose"/-->
<!--Add mover_name="structreport"/-->
<!--Add mover_name="restore_backrub_pose"/-->
<!--Add mover_name="load_br_bound_pose"/-->
<Add mover_name="mutate"/>
<Add mover_name="repack"/>
<Add mover_name="addcst"/>
<Add mover_name="minimize"/>
<Add mover_name="clearcst"/>
<Add mover_name="structreport"/>
<Add mover_name="int_ddG_mover"/>
</ParsedProtocol>
<BackrubProtocol name="backrub" mc_kt="1.2" ntrials="%%number_backrub_trials%%" pivot_residue_selector="restore_interface_shell" task_operations="restrict_to_repacking,commandline_init,extrachizero" recover_low="0" trajectory_stride="%%backrub_trajectory_stride%%" trajectory_apply_mover="finish_ddg_post_backrub"/>
</MOVERS>
<APPLY_TO_POSE>
</APPLY_TO_POSE>
<PROTOCOLS>
<Add mover_name="save_wt_bound_pose"/>
<Add mover_name="load_br_bound_pose"/>
<Add mover_name="addcst"/>
<Add mover_name="apply_score"/> <!-- Necessary to initialize neighbor graph -->
<Add mover_name="interface_shell_storer"/>
<Add mover_name="minimize"/>
<Add mover_name="clearcst"/>
<Add mover_name="backrub"/>
</PROTOCOLS>
<OUTPUT />
</ROSETTASCRIPTS>