OneScience-Group/flex_ddG_tutorial

1<ROSETTASCRIPTS>2  <SCOREFXNS>3    <ScoreFunction name="fa_talaris2014" weights="talaris2014"/>4    <ScoreFunction name="fa_talaris2014_cst" weights="talaris2014">5      <Reweight scoretype="atom_pair_constraint" weight="1.0"/>6      <Set fa_max_dis="9.0"/>7    </ScoreFunction>8  </SCOREFXNS>9 10  <!-- ### Only required input file (other than PDB) - mutation resfile ### -->11  <!-- #### All residues must be set to be NATAA packable at top of resfile ### -->12  <TASKOPERATIONS>13    <ReadResfile name="res_mutate" filename="%%mutate_resfile_relpath%%"/>14  </TASKOPERATIONS>15 16  <RESIDUE_SELECTORS>17    <Task name="resselector" fixed="0" packable="0" designable="1" task_operations="res_mutate"/>18    <Neighborhood name="bubble" selector="resselector" distance="8.0"/>19    <PrimarySequenceNeighborhood name="bubble_adjacent" selector="bubble" lower="1" upper="1"/>20    <StoredResidueSubset name="restore_neighbor_shell" subset_name="neighbor_shell"/>21    <Not name="everythingelse" selector="restore_neighbor_shell"/>22  </RESIDUE_SELECTORS>23  <TASKOPERATIONS>24    <OperateOnResidueSubset name="repackonly" selector="restore_neighbor_shell">25      <RestrictToRepackingRLT/>26    </OperateOnResidueSubset>27    <OperateOnResidueSubset name="norepack" selector="everythingelse">28      <PreventRepackingRLT/>29    </OperateOnResidueSubset>30    <UseMultiCoolAnnealer name="multicool" states="6"/>31    <ExtraChiCutoff name="extrachizero" extrachi_cutoff="0"/>32    <InitializeFromCommandline name="commandline_init"/>33    <RestrictToRepacking name="restrict_to_repacking"/>34  </TASKOPERATIONS>35 36  <FILTERS>37  </FILTERS>38 39  <MOVERS>40    <StoreResidueSubset name="neighbor_shell_storer" subset_name="neighbor_shell" residue_selector="bubble_adjacent" />41 42    <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"/>43    <ClearConstraintsMover name="clearcst"/>44    <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%%"/>45 46    <PackRotamersMover name="repack" scorefxn="fa_talaris2014" task_operations="commandline_init,repackonly,norepack,multicool"/>47    <PackRotamersMover name="mutate" scorefxn="fa_talaris2014" task_operations="commandline_init,res_mutate,norepack,multicool"/>48 49    <ReportToDB name="dbreport" batch_description="interface_ddG" database_name="ddG.db3">50      <ScoreTypeFeatures/>51      <ScoreFunctionFeatures scorefxn="fa_talaris2014"/>52      <StructureScoresFeatures scorefxn="fa_talaris2014"/>53    </ReportToDB>54 55    <ReportToDB name="structreport" batch_description="interface_ddG_struct" database_name="struct.db3">56      <PoseConformationFeatures/>57      <PdbDataFeatures/>58      <JobDataFeatures/>59      <ResidueFeatures/>60      <PoseCommentsFeatures/>61      <ProteinResidueConformationFeatures/>62      <ResidueConformationFeatures/>63    </ReportToDB>64 65    <SavePoseMover name="save_wt_bound_pose" restore_pose="0" reference_name="wt_bound_pose"/>66    <SavePoseMover name="save_backrub_pose" restore_pose="0" reference_name="backrubpdb"/>67    <SavePoseMover name="restore_backrub_pose" restore_pose="1" reference_name="backrubpdb"/>68 69    <InterfaceDdGMover name="int_ddG_mover" wt_ref_savepose_mover="save_wt_bound_pose" chain_name="%%chainstomove%%" db_reporter="dbreport" scorefxn="fa_talaris2014"/>70 71    <ScoreMover name="apply_score" scorefxn="fa_talaris2014_cst" verbose="0"/>72 73    <!-- This ParsedProtocol allows the ddG calculation to take place multiple times along the backrub trajectory, if desired -->74    <ParsedProtocol name="finish_ddg_post_backrub">75      <Add mover_name="save_backrub_pose"/>76      <Add mover_name="structreport"/>77 78      <Add mover_name="repack"/>79 80      <Add mover_name="addcst"/>81      <Add mover_name="minimize"/>82      <Add mover_name="clearcst"/>83 84      <Add mover_name="save_wt_bound_pose"/>85      <Add mover_name="structreport"/>86      <Add mover_name="restore_backrub_pose"/>87 88      <Add mover_name="mutate"/>89 90      <Add mover_name="addcst"/>91      <Add mover_name="minimize"/>92      <Add mover_name="clearcst"/>93      <Add mover_name="structreport"/>94 95      <Add mover_name="int_ddG_mover"/>96    </ParsedProtocol>97 98    <BackrubProtocol name="backrub" mc_kt="1.2" ntrials="%%number_backrub_trials%%" pivot_residue_selector="restore_neighbor_shell" task_operations="restrict_to_repacking,commandline_init,extrachizero" recover_low="0" trajectory_stride="%%backrub_trajectory_stride%%" trajectory_apply_mover="finish_ddg_post_backrub"/>99 100  </MOVERS>101  <APPLY_TO_POSE>102  </APPLY_TO_POSE>103  <PROTOCOLS>104    <Add mover_name="addcst"/>105    <Add mover_name="apply_score"/> <!-- Necessary to initialize neighbor graph -->106    <Add mover_name="neighbor_shell_storer"/>107 108    <Add mover_name="minimize"/>109    <Add mover_name="clearcst"/>110 111    <Add mover_name="backrub"/>112  </PROTOCOLS>113  <OUTPUT />114</ROSETTASCRIPTS>115