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how to run ala_scan.xml

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how to run ala_scan.xml
#1

HI,

I am running ala_scan.xml. it looks like that it calculated the difference of binding energy but not scan the interface. and I am wondering why the process was stopped in the middle. Could someone please help me. I just started learning to use Rosetta. I would very much appreciated.

 

rosetta_scripts.default.linuxgccrelease -s my.pdb -parser:protocol ala_scan.xml -database ~/rosettadatabase -ex1 -ex2 -use_input_sc

protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed dreria_com_4.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB dreria_com_4.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.66 seconds.
core.import_pose.import_pose: File 'dreria_com_4.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ALA:CtermProteinFull 6
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=ala_scan.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:

<ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="interface" weights="interface"/>
        </SCOREFXNS>
        <FILTERS>
                <AlaScan interface_distance_cutoff="10.0" name="scan" partner1="1" partner2="1" repeats="5" scorefxn="interface"/>
                <Ddg confidence="0" name="ddg"/>
                <Sasa confidence="0" name="sasa"/>
        </FILTERS>
        <MOVERS>
                <Docking fullatom="1" local_refine="1" name="dock" score_high="soft_rep"/>
        </MOVERS>
        <APPLY_TO_POSE/>
        <PROTOCOLS>
                <Add filter_name="scan" mover_name="dock"/>
                <Add filter_name="ddg"/>
                <Add filter_name="sasa"/>
     </PROTOCOLS>

.......

.. ...

......

basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.370832 0.387152 -0.844155 -0.908095 0.0392471 0.41692 0.194542 0.92118 0.337017 2.87595 25.8801 -26.0228
protocols.moves.RigidBodyMover: Translate: Jump (after):  RT -0.370832 0.387152 -0.844155 -0.908095 0.0392471 0.41692 0.194542 0.92118 0.337017 88.3949 745.888 -714.699
protocols.docking.DockingProtocol.metrics: unbound pose:
protocols.docking.DockingProtocol.metrics:
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       1.000   -1134.578   -1134.578
 fa_rep                       0.550     341.224     187.673
 fa_sol                       1.000     688.078     688.078
 fa_intra_rep                 0.005     417.770       2.089
 fa_intra_sol_xover4          1.000      38.846      38.846
 lk_ball_wtd                  1.000     -24.935     -24.935
 fa_elec                      1.000    -242.936    -242.936
 pro_close                    1.250      10.847      13.558
 hbond_sr_bb                  1.000     -17.120     -17.120
 hbond_lr_bb                  1.000     -88.091     -88.091
 hbond_bb_sc                  1.000     -36.494     -36.494
 hbond_sc                     1.000     -12.927     -12.927
 dslf_fa13                    1.250       0.000       0.000
 omega                        0.400     109.223      43.689
 fa_dun                       0.700     594.613     416.229
 p_aa_pp                      0.600     -83.080     -49.848
 yhh_planarity                0.625       0.000       0.000
 ref                          1.000      49.722      49.722
 rama_prepro                  0.450       0.375       0.169
---------------------------------------------------
 Total weighted score:                     -166.875
protocols.docking.DockingProtocol.metrics: bound pose:
protocols.docking.DockingProtocol.metrics:
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       1.000   -1170.856   -1170.856
 fa_rep                       0.550     467.280     257.004
 fa_sol                       1.000     707.382     707.382
 fa_intra_rep                 0.005     417.770       2.089
 fa_intra_sol_xover4          1.000      38.846      38.846
 lk_ball_wtd                  1.000     -24.185     -24.185
 fa_elec                      1.000    -240.783    -240.783
 pro_close                    1.250      10.847      13.558
 hbond_sr_bb                  1.000     -17.120     -17.120
 hbond_lr_bb                  1.000     -88.091     -88.091
 hbond_bb_sc                  1.000     -37.552     -37.552
 hbond_sc                     1.000     -12.927     -12.927
 dslf_fa13                    1.250       0.000       0.000
 omega                        0.400     109.223      43.689
 fa_dun                       0.700     594.613     416.229
 p_aa_pp                      0.600     -83.080     -49.848
 yhh_planarity                0.625       0.000       0.000
 ref                          1.000      49.722      49.722
 rama_prepro                  0.450       0.375       0.169
---------------------------------------------------
 Total weighted score:                     -112.673
protocols.docking.DockingProtocol.metrics: unbound energy: -166.875
protocols.docking.DockingProtocol.metrics: bound energy: -112.673
protocols.docking.DockingProtocol.metrics: interaction energy: 54.2021
protocols.docking.DockingProtocol.metrics: rb_jump: 1
protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.370832 0.387152 -0.844155 -0.908095 0.0392471 0.41692 0.194542 0.92118 0.337017 2.87595 25.8801 -26.0228
protocols.moves.RigidBodyMover: Translate: Jump (after):  RT -0.370832 0.387152 -0.844155 -0.908095 0.0392471 0.41692 0.194542 0.92118 0.337017 88.3949 745.888 -714.699
protocols.docking.DockingProtocol.metrics: unbound pose:
protocols.docking.DockingProtocol.metrics:

------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.800   -1134.578    -907.663
 fa_rep                       0.657     112.959      74.214
 fa_sol                       0.648     688.078     445.875
 pro_close                    1.000      10.847      10.847
 fa_pair                      0.452     -34.839     -15.747
 hbond_sr_bb                  0.857     -17.120     -14.672
 hbond_lr_bb                  0.857     -88.091     -75.494
 hbond_bb_sc                  0.857     -26.117     -22.383
 hbond_sc                     0.857      -9.449      -8.098
 dslf_ss_dst                  0.500       0.000       0.000
 dslf_cs_ang                  2.000       0.000       0.000
 dslf_ss_dih                  5.000       0.000       0.000
 dslf_ca_dih                  5.000       0.000       0.000
 fa_dun                       0.569     594.613     338.335
 p_aa_pp                      0.915     -83.080     -76.018
 ref                          1.000     -43.542     -43.542
---------------------------------------------------
 Total weighted score:                     -294.347
protocols.docking.DockingProtocol.metrics: bound pose:
protocols.docking.DockingProtocol.metrics:

------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       0.800   -1170.856    -936.685
 fa_rep                       0.657     120.708      79.305
 fa_sol                       0.648     707.382     458.384
 pro_close                    1.000      10.847      10.847
 fa_pair                      0.452     -37.118     -16.777
 hbond_sr_bb                  0.857     -17.120     -14.672
 hbond_lr_bb                  0.857     -88.091     -75.494
 hbond_bb_sc                  0.857     -27.231     -23.337
 hbond_sc                     0.857      -9.619      -8.244
 dslf_ss_dst                  0.500       0.000       0.000
 dslf_cs_ang                  2.000       0.000       0.000
 dslf_ss_dih                  5.000       0.000       0.000
 dslf_ca_dih                  5.000       0.000       0.000
 fa_dun                       0.569     594.613     338.335
 p_aa_pp                      0.915     -83.080     -76.018
 ref                          1.000     -43.542     -43.542
---------------------------------------------------
 Total weighted score:                     -307.899
protocols.docking.DockingProtocol.metrics: unbound energy: -294.347
protocols.docking.DockingProtocol.metrics: bound energy: -307.899
protocols.docking.DockingProtocol.metrics: interaction energy: -13.5521
protocols.docking.DockingProtocol.metrics: rb_jump: 1
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER scan=======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER scan=======================
protocols.rosetta_scripts.ParsedProtocol: Mover Docking reports failure!
protocols.jd2.JobDistributor: [ WARNING ] dreria_com_4_0001 reported failure 1 times and will no longer retry (permanent failure)
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 24 seconds
Error: [ ERROR ] Exception caught by rosetta_scripts application:
File: src/protocols/jd2/JobDistributor.cc:329
1 jobs failed; check output for error messages
Error: [ ERROR ]
                    

Post Situation: 
Mon, 2019-08-26 09:38
xinmiaohe