OneScience-Group/flex_ddG_tutorial

1<ROSETTASCRIPTS>2  <SCOREFXNS>3    <ScoreFunction name="fa_fxn" weights="talaris2014">4    </ScoreFunction>5    <ScoreFunction name="fa_fxn_cst" weights="talaris2014">6      <Reweight scoretype="atom_pair_constraint" weight="1.0"/>7      <Set fa_max_dis="9.0"/>8    </ScoreFunction>9  </SCOREFXNS>10 11  <!-- ### Only required input - mutation resfile ### -->12  <!-- #### All residues must be set to be NATAA packable at top of resfile ### -->13  <TASKOPERATIONS>14    <ReadResfile name="res_mutate" filename="%%mutate_resfile_relpath%%"/>15  </TASKOPERATIONS>16 17  <RESIDUE_SELECTORS>18    <Task name="resselector" fixed="0" packable="0" designable="1" task_operations="res_mutate"/>19    <Neighborhood name="bubble" selector="resselector" distance="%%neighbor_distance%%" include_focus_in_subset="true"/>20    <PrimarySequenceNeighborhood name="bubble_adjacent" selector="bubble" lower="1" upper="1"/>21    <StoredResidueSubset name="restore_neighbor_shell" subset_name="neighbor_shell"/>22    <Not name="everythingelse" selector="restore_neighbor_shell"/>23  </RESIDUE_SELECTORS>24  <TASKOPERATIONS>25    <OperateOnResidueSubset name="repackonly" selector="restore_neighbor_shell">26      <RestrictToRepackingRLT/>27    </OperateOnResidueSubset>28    <OperateOnResidueSubset name="norepack" selector="everythingelse">29      <PreventRepackingRLT/>30    </OperateOnResidueSubset>31    <UseMultiCoolAnnealer name="multicool" states="6"/>32    <ExtraChiCutoff name="extrachizero" extrachi_cutoff="0"/>33    <InitializeFromCommandline name="commandline_init"/>34    <RestrictToRepacking name="restrict_to_repacking"/>35  </TASKOPERATIONS>36 37  <FILTERS>38  </FILTERS>39 40  <MOVERS>41    <StoreResidueSubset name="neighbor_shell_storer" subset_name="neighbor_shell" residue_selector="bubble_adjacent" />42 43    <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"/>44    <ClearConstraintsMover name="clearcst"/>45    <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%%"/>46 47    <PackRotamersMover name="repack" scorefxn="fa_fxn" task_operations="commandline_init,repackonly,norepack,multicool"/>48 49    <SavePoseMover name="input_struct_spm" reference_name="input_struct"/>50    <SavePoseMover name="input_struct_lpm" restore_pose="1" reference_name="input_struct"/>51    <SavePoseMover name="min_input_struct_spm" reference_name="min_input_struct"/>52    <SavePoseMover name="min_input_struct_lpm" restore_pose="1" reference_name="min_input_struct"/>53 54    <ReportToDB name="structreport" batch_description="interface_ddG_struct" database_name="struct.db3">55      <PoseConformationFeatures/>56      <PdbDataFeatures/>57      <JobDataFeatures/>58      <ResidueFeatures/>59      <PoseCommentsFeatures/>60      <ProteinResidueConformationFeatures/>61      <ResidueConformationFeatures/>62      <RotamerFeatures/>63      <ResidueBurialFeatures/>64      <ProteinRMSDFeatures reference_name="min_input_struct"/>65    </ReportToDB>66 67    <ScoreMover name="apply_score" scorefxn="fa_fxn_cst" verbose="0"/>68 69    <PDBTrajectoryRecorder name="dump_wt_minimized" stride="1" filename="wt_minimized.pdb"/>70 71    <ParsedProtocol name="finish_wt_post_backrub">72      <Add mover_name="structreport"/>73 74      <Add mover_name="repack"/>75 76      <Add mover_name="addcst"/>77      <Add mover_name="minimize"/>78      <Add mover_name="clearcst"/>79 80      <Add mover_name="structreport"/>81      <Add mover_name="dump_wt_minimized"/>82    </ParsedProtocol>83 84    <BackrubProtocol name="backrub" mc_kt="%%backrub_kt%%" ntrials="%%backrub_trials%%" pivot_residue_selector="restore_neighbor_shell" task_operations="restrict_to_repacking,commandline_init,extrachizero" recover_low="0" trajectory_stride="%%backrub_stride%%" trajectory_apply_mover="finish_wt_post_backrub" trajectory="1" scorefxn="fa_fxn"/>85 86  </MOVERS>87  <APPLY_TO_POSE>88  </APPLY_TO_POSE>89  <PROTOCOLS>90    <Add mover_name="input_struct_spm"/>91    <Add mover_name="addcst"/>92    <Add mover_name="apply_score"/> <!-- Necessary to initialize neighbor graph -->93    <Add mover_name="neighbor_shell_storer"/>94 95    <Add mover_name="minimize"/>96 97    <Add mover_name="clearcst"/>98    <Add mover_name="min_input_struct_spm"/>99 100    <Add mover_name="input_struct_lpm"/>101    <Add mover_name="structreport"/>102    <Add mover_name="min_input_struct_lpm"/>103    <Add mover_name="structreport"/>104 105    <Add mover_name="backrub"/>106  </PROTOCOLS>107  <OUTPUT />108</ROSETTASCRIPTS>109