Error with docking_prepack_protocol while executing the tutorial "Docking Flexible Proteins"

1 post / 0 new

Top

Hello!
I'm new at Rosetta and was doing the tutorials for protein-protein docking. I execute the command below with no problems:

$>$ROSETTA3/main/source/bin/docking_prepack_protocol.linuxgccrelease @flag_ensemble_prepack

core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.linux.release-356 r356 2023.35+release.23439d3 23439d33534e3f106f2ad301c8c3c56013ca8471 https://www.rosettacommons.org 2023-09-02T00:12:54.400843
core.init: command: /home/vitor/Rosetta/main/source/bin/docking_prepack_protocol.linuxgccrelease @flag_ensemble_prepack
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-341847908 seed_offset=0 real_seed=-341847908
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-341847908 RG_type=mt19937
core.init: found database environment variable ROSETTA3_DB: /home/vitor/Rosetta/main/database
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.665212 seconds.
basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input_files/col_complex.pdb nstruct index 1
core.import_pose.import_pose: File 'input_files/1v74.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 107
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 194
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input_files/col_complex.pdb
core.import_pose.import_pose: File 'input_files/col_complex.pdb' automatically determined to be of type PDB
core.pack.rotamer_set.UnboundRotamersOperation: Adding 'unbound' rotamers from input_files/col_complex.pdb
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
protocols.docking.DockingEnsemblePrepackProtocol: Ensemble 1: COL_D_ensemblelist.ensemble
protocols.moves.DockingEnsemble: Loading Ensemble
core.import_pose.import_pose: File 'input_files/COL_D_ensemble/COL_D_0001.pdb' automatically determined to be of type PDB
core.import_pose.import_pose: File 'input_files/COL_D_ensemble/COL_D_0002.pdb' automatically determined to be of type PDB
core.import_pose.import_pose: File 'input_files/COL_D_ensemble/COL_D_0003.pdb' automatically determined to be of type PDB
core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.014521 seconds.
protocols.moves.DockingEnsemble: ensemble summary: start_res_ 1 end_res_ 107 conf_size_ 107 ensemble_size_ 3
protocols.docking.DockingEnsemblePrepackProtocol: Ensemble 2: IMM_D_ensemblelist.ensemble
protocols.moves.DockingEnsemble: Loading Ensemble
core.import_pose.import_pose: File 'input_files/IMM_D_ensemble/IMM_D_0001.pdb' automatically determined to be of type PDB
core.import_pose.import_pose: File 'input_files/IMM_D_ensemble/IMM_D_0002.pdb' automatically determined to be of type PDB
core.import_pose.import_pose: File 'input_files/IMM_D_ensemble/IMM_D_0003.pdb' automatically determined to be of type PDB
protocols.moves.DockingEnsemble: ensemble summary: start_res_ 108 end_res_ 194 conf_size_ 87 ensemble_size_ 3
core.pose.subpose_manipulation_util: FOLD_TREE EDGE 1 88 -1 EDGE 88 107 -1 EDGE 88 158 1 EDGE 158 108 -1 EDGE 158 194 -1
FOLD_TREE EDGE 1 88 -1 EDGE 88 107 -1
FOLD_TREE EDGE 51 1 -1 EDGE 51 87 -1
core.import_pose.import_pose: File 'partner1_temp.pdb' automatically determined to be of type PDB
core.import_pose.import_pose: File 'partner2_temp.pdb' automatically determined to be of type PDB
protocols.relax.RelaxScriptManager: Reading relax scripts list from database.
protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt
protocols.relax.RelaxScriptManager: ================== Reading script file: /home/vitor/Rosetta/main/database/sampling/relax_scripts/MonomerRelax2019.txt ==================
protocols.relax.RelaxScriptManager: repeat %%nrepeats%%
protocols.relax.RelaxScriptManager: coord_cst_weight 1.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.040
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.051
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.5
protocols.relax.RelaxScriptManager: scale:fa_rep 0.265
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.280
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.559
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.581
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 1
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: min 0.00001
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/vitor/Rosetta/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/vitor/Rosetta/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.132677 seconds to load from binary
protocols.relax.FastRelax: CMD: repeat -286.938 0 0 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight -286.938 0 0 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep -346.01 0 0 0.022
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 3735 rotamers at 107 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -358.227 0 0 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -355.785 0 0 0.02805
protocols.relax.FastRelax: CMD: min -426.966 0.875475 0.875475 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -426.966 0.875475 0.875475 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -288.779 0.875475 0.875475 0.14575
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 3312 rotamers at 107 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -318.532 0.875475 0.875475 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -311.635 0.875475 0.875475 0.154
protocols.relax.FastRelax: CMD: min -366.542 0.54839 0.54839 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -366.542 0.54839 0.54839 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -325.034 0.54839 0.54839 0.30745
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 3123 rotamers at 107 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -327.787 0.54839 0.54839 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -324.691 0.54839 0.54839 0.31955
protocols.relax.FastRelax: CMD: min -340.305 0.405651 0.405651 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -340.305 0.405651 0.405651 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -303.143 0.405651 0.405651 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 3052 rotamers at 107 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -303.303 0.405651 0.405651 0.55
protocols.relax.FastRelax: CMD: min -326.502 0.428665 0.428665 0.55
protocols.relax.FastRelax: MRP: 0 -326.502 -326.502 0.428665 0.428665
protocols.relax.FastRelax: CMD: accept_to_best -326.502 0.428665 0.428665 0.55
protocols.relax.FastRelax: CMD: endrepeat -326.502 0.428665 0.428665 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.relax.FastRelax: CMD: repeat -235.515 12.7182 0 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight -235.515 12.7182 0 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep -287.251 12.7182 0 0.022
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 1798 rotamers at 87 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -300.717 12.7182 0 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -299.198 12.7182 0 0.02805
protocols.relax.FastRelax: CMD: min -390.613 12.5033 0.874736 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -390.613 12.5033 0.874736 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -228.474 12.5033 0.874736 0.14575
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 1808 rotamers at 87 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -256.837 12.5033 0.874736 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -247.943 12.5033 0.874736 0.154
protocols.relax.FastRelax: CMD: min -331.242 12.5863 0.644631 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -331.242 12.5863 0.644631 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -287.929 12.5863 0.644631 0.30745
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 1650 rotamers at 87 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -288.017 12.5863 0.644631 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -284.635 12.5863 0.644631 0.31955
protocols.relax.FastRelax: CMD: min -296.141 12.6413 0.557175 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -296.141 12.6413 0.557175 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -256.251 12.6413 0.557175 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 1565 rotamers at 87 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -256.022 12.6413 0.557175 0.55
protocols.relax.FastRelax: CMD: min -272.256 12.6715 0.550035 0.55
protocols.relax.FastRelax: MRP: 0 -272.256 -272.256 12.6715 0.550035
protocols.relax.FastRelax: CMD: accept_to_best -272.256 12.6715 0.550035 0.55
protocols.relax.FastRelax: CMD: endrepeat -272.256 12.6715 0.550035 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 3101 rotamers at 107 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.moves.DockingEnsemble: score_high: -325.565
protocols.moves.DockingEnsemble: filename: input_files/COL_D_ensemble/partner1_starting_conf.pdb.ppk
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 1474 rotamers at 87 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.moves.DockingEnsemble: score_high: -271.907
protocols.moves.DockingEnsemble: filename: input_files/IMM_D_ensemble/partner2_starting_conf.pdb.ppk
protocols.moves.DockingEnsemble: score_low: -5.13425
protocols.moves.DockingEnsemble: score_low: -5.13425
protocols.moves.DockingEnsemble: score_low: -4.26693
core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes.
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 2950 rotamers at 107 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.moves.DockingEnsemble: score_high: -296.322
protocols.moves.DockingEnsemble: filename: input_files/COL_D_ensemble/COL_D_0001.pdb.ppk
protocols.moves.DockingEnsemble: filename in array: input_files/COL_D_ensemble/COL_D_0001.pdb.ppk
core.util.switchresiduetypeset: [ WARNING ] When switching to a centroid ResidueTypeSet: Pose already contains centroid ResidueTypes.
protocols.moves.DockingEnsemble: score_low: -5.03751
core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes.
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 2994 rotamers at 107 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.moves.DockingEnsemble: score_high: -298.784
protocols.moves.DockingEnsemble: filename: input_files/COL_D_ensemble/COL_D_0002.pdb.ppk
protocols.moves.DockingEnsemble: filename in array: input_files/COL_D_ensemble/COL_D_0002.pdb.ppk
core.util.switchresiduetypeset: [ WARNING ] When switching to a centroid ResidueTypeSet: Pose already contains centroid ResidueTypes.
protocols.moves.DockingEnsemble: score_low: -4.03374
core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes.
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 2982 rotamers at 107 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.moves.DockingEnsemble: score_high: -299.492
protocols.moves.DockingEnsemble: filename: input_files/COL_D_ensemble/COL_D_0003.pdb.ppk
protocols.moves.DockingEnsemble: filename in array: input_files/COL_D_ensemble/COL_D_0003.pdb.ppk
protocols.docking.DockingEnsemblePrepackProtocol: outside the first ensemble loop
protocols.moves.DockingEnsemble: input_files/COL_D_ensemble/COL_D_0001.pdb.ppk

protocols.moves.DockingEnsemble: input_files/COL_D_ensemble/COL_D_0002.pdb.ppk

protocols.moves.DockingEnsemble: input_files/COL_D_ensemble/COL_D_0003.pdb.ppk

protocols.moves.DockingEnsemble: score_low: -6.63069
core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes.
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 1573 rotamers at 87 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.moves.DockingEnsemble: score_high: -249.23
protocols.moves.DockingEnsemble: filename: input_files/IMM_D_ensemble/IMM_D_0001.pdb.ppk
protocols.moves.DockingEnsemble: filename in array: input_files/IMM_D_ensemble/IMM_D_0001.pdb.ppk
core.util.switchresiduetypeset: [ WARNING ] When switching to a centroid ResidueTypeSet: Pose already contains centroid ResidueTypes.
protocols.moves.DockingEnsemble: score_low: -6.46975
core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes.
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 1509 rotamers at 87 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.moves.DockingEnsemble: score_high: -246.303
protocols.moves.DockingEnsemble: filename: input_files/IMM_D_ensemble/IMM_D_0002.pdb.ppk
protocols.moves.DockingEnsemble: filename in array: input_files/IMM_D_ensemble/IMM_D_0002.pdb.ppk
core.util.switchresiduetypeset: [ WARNING ] When switching to a centroid ResidueTypeSet: Pose already contains centroid ResidueTypes.
protocols.moves.DockingEnsemble: score_low: -5.34301
core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes.
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 1470 rotamers at 87 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.moves.DockingEnsemble: score_high: -243.888
protocols.moves.DockingEnsemble: filename: input_files/IMM_D_ensemble/IMM_D_0003.pdb.ppk
protocols.moves.DockingEnsemble: filename in array: input_files/IMM_D_ensemble/IMM_D_0003.pdb.ppk
protocols.docking.DockingEnsemblePrepackProtocol: outside the second ensemble loop
protocols.moves.DockingEnsemble: input_files/IMM_D_ensemble/IMM_D_0001.pdb.ppk

protocols.moves.DockingEnsemble: input_files/IMM_D_ensemble/IMM_D_0002.pdb.ppk

protocols.moves.DockingEnsemble: input_files/IMM_D_ensemble/IMM_D_0003.pdb.ppk

core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4674 rotamers at 194 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.jd2.JobDistributor: col_complex_ensemble_prepack_0001 reported success in 39 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 39 seconds
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

But, as I followed through the second command, I got the following error:

$>$ROSETTA3/main/source/bin/docking_protocol.linuxgccrelease @flag_ensemble_docking

ERROR: The ensembles must be prepacked using the docking_prepack_protocol executable to run EnsembleDock!
ERROR:: Exit from: src/protocols/docking/DockingProtocol.cc line: 597
protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job col_complex_ensemble_dock_0001

[ ERROR ]: Caught exception:

File: src/protocols/docking/DockingProtocol.cc:597
[ ERROR ] UtilityExitException
ERROR: The ensembles must be prepacked using the docking_prepack_protocol executable to run EnsembleDock!

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

protocols.jd2.JobDistributor: [ WARNING ] col_complex_ensemble_dock_0001 reported failure and will NOT retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 0 seconds

---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
1 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
The content of the ROSETTA_CRASH.log follows below:

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2023.35+release.23439d3
[COMMIT_DATE]: 2023-09-02T00:12:54.400843
[APPLICATION]: /home/vitor/Rosetta/main/source/bin/docking_protocol.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "11.4.0"
[STDLIB]: libstdc++ version 20230528
[START_OPTIONS]
-in:file:s=input_files/col_complex.pdb -in:file:native=input_files/1v74.pdb -out:nstruct=1 -out:suffix=_ensemble_dock -out:path:all=output_files/ -packing:unboundrot=input_files/col_complex.pdb -packing:ex1 -packing:ex2aro -docking:partners=A_B -docking:dock_pert=3 8 -docking:ensemble1=COL_D_ensemblelist -docking:ensemble2=IMM_D_ensemblelist

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/vitor/Rosetta/main/source/build/src/release/linux/6.5/64/x86/gcc/11/default/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f7306f7397a]
/home/vitor/Rosetta/main/source/build/src/release/linux/6.5/64/x86/gcc/11/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f7306ebb1f0]
/home/vitor/Rosetta/main/source/build/src/release/linux/6.5/64/x86/gcc/11/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f7306f787e3]
/home/vitor/Rosetta/main/source/build/src/release/linux/6.5/64/x86/gcc/11/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f7306f785ab]
/home/vitor/Rosetta/main/source/build/src/release/linux/6.5/64/x86/gcc/11/default/libprotocols_h.5.so(protocols::docking::DockingProtocol::finalize_setup(core::pose::Pose&)+0x318a) [0x7f730899797a]
/home/vitor/Rosetta/main/source/build/src/release/linux/6.5/64/x86/gcc/11/default/libprotocols_h.5.so(protocols::docking::DockingProtocol::apply(core::pose::Pose&)+0x1b8) [0x7f7308997ea8]
/home/vitor/Rosetta/main/source/build/src/release/linux/6.5/64/x86/gcc/11/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe57) [0x7f7308346c87]
/home/vitor/Rosetta/main/source/build/src/release/linux/6.5/64/x86/gcc/11/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f7308348c98]
/home/vitor/Rosetta/main/source/build/src/release/linux/6.5/64/x86/gcc/11/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f73083318b9]
/home/vitor/Rosetta/main/source/bin/docking_protocol.linuxgccrelease(+0x3fa5) [0x55b9ab25afa5]
/home/vitor/Rosetta/main/source/bin/docking_protocol.linuxgccrelease(+0x38a0) [0x55b9ab25a8a0]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f7306429d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f7306429e40]
/home/vitor/Rosetta/main/source/bin/docking_protocol.linuxgccrelease(+0x3a25) [0x55b9ab25aa25]

[END_BACKTRACE]

[FILE]: src/protocols/docking/DockingProtocol.cc
[LINE]: 597
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: using the docking_prepack_protocol executable to run EnsembleDock!

[END_MESSAGE]
[END_CRASH_REPORT]
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
I don't see why docking_prepack_protocol is not being recognized in the second command, since it run perfectly at the beginning. What could be wrong? Is related to some update in the tutorial files?
For clarification, I'm executing all the commands in /home/user/Rosetta/main/demos/tutorials/Protein-Protein-Docking

Thanks in advance for the attention!

Category:

Docking

Post Situation:

Unsolved

Mon, 2023-11-06 09:43

vitoralmeida1808

Search form

You are here

Error with docking_prepack_protocol while executing the tutorial "Docking Flexible Proteins"