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August 26, 2019 at 4:38 pm #3232
Anonymous
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 ]
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