Hi, sorry for disturbing you but I have problems about samll ligand docking in Ubuntu 20.04. It occurs errors when I followed jens Meiler's toturial about small ligand docking.
command line:
$ ~/Desktop/rosetta_workshop/rosetta/main/source/bin/rosetta_scripts.mpi.linuxgccrelease @options.txt -nstruct 5 -database ~/Desktop/rosetta_workshop/rosetta/main/database/
core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags
core.init: (0) Rosetta version: rosetta.binary.linux.release-296 r296 2021.36+release.57ac713 57ac713a6e1d8ce6f60269b3988b1adac1d96fc6 https://www.rosettacommons.org 2021-09-12T14:23:57.882909
core.init: (0) command: /home/zhengjishen/Desktop/rosetta_workshop/rosetta/main/source/bin/rosetta_scripts.mpi.linuxgccrelease @options.txt -nstruct 5 -database /home/zhengjishen/Desktop/rosetta_workshop/rosetta/main/database/
basic.random.init_random_generator: (0) 'RNG device' seed mode, using '/dev/urandom', seed=1225880350 seed_offset=0 real_seed=1225880350
basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=1225880350 RG_type=mt19937
protocols.jd2.PDBJobInputter: (0) Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: (0) pushed 3PBL_A.pdb nstruct indices 1 - 5
protocols.jd2.PDBJobInputter: (0) pushed ETQ.pdb nstruct indices 1 - 5
protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active ...
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from PDB 3PBL_A.pdb
core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set. Created 75 residue types
core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 0.030769 seconds.
core.import_pose.import_pose: (0) File '3PBL_A.pdb' automatically determined to be of type PDB
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE2 on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OG on residue SER 114
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OG1 on residue THR 389
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG2 on residue THR 389
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OXT on residue CYS:CtermProteinFull 432
core.conformation.Conformation: (0) Found disulfide between residues 72 150
core.conformation.Conformation: (0) current variant for 72 CYS
core.conformation.Conformation: (0) current variant for 150 CYS
core.conformation.Conformation: (0) current variant for 72 CYD
core.conformation.Conformation: (0) current variant for 150 CYD
core.conformation.Conformation: (0) Found disulfide between residues 387 390
core.conformation.Conformation: (0) current variant for 387 CYS
core.conformation.Conformation: (0) current variant for 390 CYS
core.conformation.Conformation: (0) current variant for 387 CYD
core.conformation.Conformation: (0) current variant for 390 CYD
core.pack.pack_missing_sidechains: (0) packing residue number 113 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 114 because of missing atom number 6 atom name OG
core.pack.pack_missing_sidechains: (0) packing residue number 297 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 389 because of missing atom number 6 atom name OG1
core.pack.task: (0) Packer task: initialize from command line()
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
core.scoring.etable: (0) Starting energy table calculation
core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: (0) Finished calculating energy tables.
basic.io.database: (0) Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/score12_params/HBPoly1D.csv
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/score12_params/HBFadeIntervals.csv
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/score12_params/HBEval.csv
basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
basic.io.database: (0) Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4
basic.io.database: (0) Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score
core.pack.dunbrack.RotamerLibrary: (0) Using Dunbrack library binary file '/home/zhengjishen/Desktop/rosetta_workshop/rosetta/main/database/rotamer/bbdep02.May.sortlib.Dunbrack02.lib.bin'.
core.pack.dunbrack.RotamerLibrary: (0) Dunbrack library took 0.032956 seconds to load from binary
core.pack.pack_rotamers: (0) built 87 rotamers at 4 positions.
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
core.pack.task: (0) Packer task: initialize from command line()
core.pack.pack_rotamers: (0) built 1029 rotamers at 432 positions.
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 16 ASN ASN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 66 ASN ASN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 89 ASN ASN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 3 position: 108 GLN GLN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 329 ASN ASN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 386 HIS HIS
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 3 position: 388 GLN GLN
protocols.rosetta_scripts.RosettaScriptsParser: (0) dock_design_filename=dock.xml
protocols.rosetta_scripts.RosettaScriptsParser: (0) Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: (0) ...done
protocols.rosetta_scripts.RosettaScriptsParser: (0) Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: (0) ...done
protocols.rosetta_scripts.RosettaScriptsParser: (0) Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: (0) ...done
protocols.rosetta_scripts.RosettaScriptsParser: (0) Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="ligand_soft_rep" weights="ligand_soft_rep"/>
<ScoreFunction name="hard_rep" weights="ligand"/>
</SCOREFXNS>
<LIGAND_AREAS>
<LigandArea add_nbr_radius="true" all_atom_mode="false" chain="X" cutoff="6.0" name="inhibitor_dock_sc"/>
<LigandArea add_nbr_radius="true" all_atom_mode="false" chain="X" cutoff="6.0" name="inhibitor_final_sc"/>
<LigandArea Calpha_restraints="0.3" add_nbr_radius="false" all_atom_mode="true" chain="X" cutoff="7.0" name="inhibitor_final_bb"/>
</LIGAND_AREAS>
<INTERFACE_BUILDERS>
<InterfaceBuilder ligand_areas="inhibitor_dock_sc" name="side_chain_for_docking"/>
<InterfaceBuilder ligand_areas="inhibitor_final_sc" name="side_chain_for_final"/>
<InterfaceBuilder extension_window="3" ligand_areas="inhibitor_final_bb" name="backbone"/>
</INTERFACE_BUILDERS>
<MOVEMAP_BUILDERS>
<MoveMapBuilder minimize_water="false" name="docking" sc_interface="side_chain_for_docking"/>
<MoveMapBuilder bb_interface="backbone" minimize_water="false" name="final" sc_interface="side_chain_for_final"/>
</MOVEMAP_BUILDERS>
<SCORINGGRIDS ligand_chain="X" width="15">
<ClassicGrid grid_name="classic" weight="1.0"/>
</SCORINGGRIDS>
<MOVERS>
<Transform angle="20" box_size="7.0" chain="X" cycles="500" move_distance="0.2" name="transform" repeats="1" temperature="5"/>
<HighResDocker cycles="6" movemap_builder="docking" name="high_res_docker" repack_every_Nth="3" scorefxn="ligand_soft_rep"/>
<FinalMinimizer movemap_builder="final" name="final" scorefxn="hard_rep"/>
<InterfaceScoreCalculator chains="X" name="add_scores" native="crystal_complex.pdb" scorefxn="hard_rep"/>
</MOVERS>
<PROTOCOLS>
<Add mover_name="transform"/>
<Add mover_name="high_res_docker"/>
<Add mover_name="final"/>
<Add mover_name="add_scores"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
core.scoring.etable: (0) Using alternate parameters: LJ_RADIUS_SOFT in Etable construction.
core.scoring.etable: (0) Starting energy table calculation
core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: (0) Finished calculating energy tables.
basic.io.database: (0) Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: (0) Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
protocols.jd2.parser.ScoreFunctionLoader: (0) defined score function "ligand_soft_rep" with weights "ligand_soft_rep"
protocols.jd2.parser.ScoreFunctionLoader: (0) defined score function "hard_rep" with weights "ligand"
protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "transform" of type Transform
protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "high_res_docker" of type HighResDocker
protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "final" of type FinalMinimizer
core.import_pose.import_pose: (0) File 'crystal_complex.pdb' automatically determined to be of type PDB
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE2 on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OG on residue SER 114
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OG1 on residue THR 389
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG2 on residue THR 389
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OXT on residue CYS:CtermProteinFull 432
core.conformation.Conformation: (0) Found disulfide between residues 72 150
core.conformation.Conformation: (0) current variant for 72 CYS
core.conformation.Conformation: (0) current variant for 150 CYS
core.conformation.Conformation: (0) current variant for 72 CYD
core.conformation.Conformation: (0) current variant for 150 CYD
core.conformation.Conformation: (0) Found disulfide between residues 387 390
core.conformation.Conformation: (0) current variant for 387 CYS
core.conformation.Conformation: (0) current variant for 390 CYS
core.conformation.Conformation: (0) current variant for 387 CYD
core.conformation.Conformation: (0) current variant for 390 CYD
core.pack.pack_missing_sidechains: (0) packing residue number 113 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 114 because of missing atom number 6 atom name OG
core.pack.pack_missing_sidechains: (0) packing residue number 297 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 389 because of missing atom number 6 atom name OG1
core.pack.task: (0) Packer task: initialize from command line()
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
core.pack.rotamers.SingleLigandRotamerLibrary: (0) Read in 58 rotamers from ETQ_conformers.pdb !
core.pack.pack_rotamers: (0) built 87 rotamers at 4 positions.
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
core.pack.task: (0) Packer task: initialize from command line()
core.pack.pack_rotamers: (0) built 1035 rotamers at 433 positions.
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 16 ASN ASN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 66 ASN ASN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 3 position: 108 GLN GLN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 329 ASN ASN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 386 HIS HIS
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 3 position: 388 GLN GLN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: proton chi angle change: chidev= 93.717 chino= 1 position: 433 ETQ ETQ
protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "add_scores" of type InterfaceScoreCalculator
protocols.rosetta_scripts.ParsedProtocol: (0) ParsedProtocol mover with the following settings
protocols.rosetta_scripts.ParsedProtocol: (0) Added mover "transform"
protocols.rosetta_scripts.ParsedProtocol: (0) Added mover "high_res_docker"
protocols.rosetta_scripts.ParsedProtocol: (0) Added mover "final"
protocols.rosetta_scripts.ParsedProtocol: (0) Added mover "add_scores"
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy 3PBL_A.pdb
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Transform - transform=======================
protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:453
chain_id X does not exist
protocols.jd2.JobDistributor: (0) [ ERROR ]
[ERROR] Exception caught by JobDistributor for job 3PBL_A_0001
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:453
chain_id X does not exist
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: (0) [ WARNING ] 3PBL_A_0001 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy 3PBL_A.pdb
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy 3PBL_A.pdb
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Transform - transform=======================
protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:453
chain_id X does not exist
protocols.jd2.JobDistributor: (0) [ ERROR ]
[ERROR] Exception caught by JobDistributor for job 3PBL_A_0002
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:453
chain_id X does not exist
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: (0) [ WARNING ] 3PBL_A_0002 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy 3PBL_A.pdb
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy 3PBL_A.pdb
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Transform - transform=======================
protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:453
chain_id X does not exist
protocols.jd2.JobDistributor: (0) [ ERROR ]
[ERROR] Exception caught by JobDistributor for job 3PBL_A_0003
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:453
chain_id X does not exist
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: (0) [ WARNING ] 3PBL_A_0003 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy 3PBL_A.pdb
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy 3PBL_A.pdb
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Transform - transform=======================
protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:453
chain_id X does not exist
protocols.jd2.JobDistributor: (0) [ ERROR ]
[ERROR] Exception caught by JobDistributor for job 3PBL_A_0004
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:453
chain_id X does not exist
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: (0) [ WARNING ] 3PBL_A_0004 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy 3PBL_A.pdb
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy 3PBL_A.pdb
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Transform - transform=======================
protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:453
chain_id X does not exist
protocols.jd2.JobDistributor: (0) [ ERROR ]
[ERROR] Exception caught by JobDistributor for job 3PBL_A_0005
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:453
chain_id X does not exist
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: (0) [ WARNING ] 3PBL_A_0005 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from PDB ETQ.pdb
core.import_pose.import_pose: (0) File 'ETQ.pdb' automatically determined to be of type PDB
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
core.pack.task: (0) Packer task: initialize from command line()
core.pack.pack_rotamers: (0) built 6 rotamers at 1 positions.
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: proton chi angle change: chidev= 93.717 chino= 1 position: 1 ETQ ETQ
protocols.rosetta_scripts.RosettaScriptsParser: (0) dock_design_filename=dock.xml
protocols.rosetta_scripts.RosettaScriptsParser: (0) Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: (0) ...done
protocols.rosetta_scripts.RosettaScriptsParser: (0) Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="ligand_soft_rep" weights="ligand_soft_rep"/>
<ScoreFunction name="hard_rep" weights="ligand"/>
</SCOREFXNS>
<LIGAND_AREAS>
<LigandArea add_nbr_radius="true" all_atom_mode="false" chain="X" cutoff="6.0" name="inhibitor_dock_sc"/>
<LigandArea add_nbr_radius="true" all_atom_mode="false" chain="X" cutoff="6.0" name="inhibitor_final_sc"/>
<LigandArea Calpha_restraints="0.3" add_nbr_radius="false" all_atom_mode="true" chain="X" cutoff="7.0" name="inhibitor_final_bb"/>
</LIGAND_AREAS>
<INTERFACE_BUILDERS>
<InterfaceBuilder ligand_areas="inhibitor_dock_sc" name="side_chain_for_docking"/>
<InterfaceBuilder ligand_areas="inhibitor_final_sc" name="side_chain_for_final"/>
<InterfaceBuilder extension_window="3" ligand_areas="inhibitor_final_bb" name="backbone"/>
</INTERFACE_BUILDERS>
<MOVEMAP_BUILDERS>
<MoveMapBuilder minimize_water="false" name="docking" sc_interface="side_chain_for_docking"/>
<MoveMapBuilder bb_interface="backbone" minimize_water="false" name="final" sc_interface="side_chain_for_final"/>
</MOVEMAP_BUILDERS>
<SCORINGGRIDS ligand_chain="X" width="15">
<ClassicGrid grid_name="classic" weight="1.0"/>
</SCORINGGRIDS>
<MOVERS>
<Transform angle="20" box_size="7.0" chain="X" cycles="500" move_distance="0.2" name="transform" repeats="1" temperature="5"/>
<HighResDocker cycles="6" movemap_builder="docking" name="high_res_docker" repack_every_Nth="3" scorefxn="ligand_soft_rep"/>
<FinalMinimizer movemap_builder="final" name="final" scorefxn="hard_rep"/>
<InterfaceScoreCalculator chains="X" name="add_scores" native="crystal_complex.pdb" scorefxn="hard_rep"/>
</MOVERS>
<PROTOCOLS>
<Add mover_name="transform"/>
<Add mover_name="high_res_docker"/>
<Add mover_name="final"/>
<Add mover_name="add_scores"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
protocols.jd2.parser.ScoreFunctionLoader: (0) defined score function "ligand_soft_rep" with weights "ligand_soft_rep"
protocols.jd2.parser.ScoreFunctionLoader: (0) defined score function "hard_rep" with weights "ligand"
protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "transform" of type Transform
protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "high_res_docker" of type HighResDocker
protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "final" of type FinalMinimizer
core.import_pose.import_pose: (0) File 'crystal_complex.pdb' automatically determined to be of type PDB
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE2 on residue GLN 113
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OG on residue SER 114
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 297
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OG1 on residue THR 389
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG2 on residue THR 389
core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OXT on residue CYS:CtermProteinFull 432
core.conformation.Conformation: (0) Found disulfide between residues 72 150
core.conformation.Conformation: (0) current variant for 72 CYS
core.conformation.Conformation: (0) current variant for 150 CYS
core.conformation.Conformation: (0) current variant for 72 CYD
core.conformation.Conformation: (0) current variant for 150 CYD
core.conformation.Conformation: (0) Found disulfide between residues 387 390
core.conformation.Conformation: (0) current variant for 387 CYS
core.conformation.Conformation: (0) current variant for 390 CYS
core.conformation.Conformation: (0) current variant for 387 CYD
core.conformation.Conformation: (0) current variant for 390 CYD
core.pack.pack_missing_sidechains: (0) packing residue number 113 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 114 because of missing atom number 6 atom name OG
core.pack.pack_missing_sidechains: (0) packing residue number 297 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: (0) packing residue number 389 because of missing atom number 6 atom name OG1
core.pack.task: (0) Packer task: initialize from command line()
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
core.pack.pack_rotamers: (0) built 87 rotamers at 4 positions.
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
core.pack.task: (0) Packer task: initialize from command line()
core.pack.pack_rotamers: (0) built 1035 rotamers at 433 positions.
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 16 ASN ASN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 66 ASN ASN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 89 ASN ASN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 3 position: 108 GLN GLN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 329 ASN ASN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 386 HIS HIS
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 3 position: 388 GLN GLN
core.io.pdb.file_data: (0) [ WARNING ] OPT-H: proton chi angle change: chidev= 93.717 chino= 1 position: 433 ETQ ETQ
protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "add_scores" of type InterfaceScoreCalculator
protocols.rosetta_scripts.ParsedProtocol: (0) ParsedProtocol mover with the following settings
protocols.rosetta_scripts.ParsedProtocol: (0) Added mover "transform"
protocols.rosetta_scripts.ParsedProtocol: (0) Added mover "high_res_docker"
protocols.rosetta_scripts.ParsedProtocol: (0) Added mover "final"
protocols.rosetta_scripts.ParsedProtocol: (0) Added mover "add_scores"
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy ETQ.pdb
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Transform - transform=======================
ERROR: Chain '1' is not directly built by any jump.
ERROR:: Exit from: src/core/pose/chains_util.cc line: 496
protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:496
[ ERROR ] UtilityExitException
ERROR: Chain '1' is not directly built by any jump.
protocols.jd2.JobDistributor: (0) [ ERROR ]
[ERROR] Exception caught by JobDistributor for job ETQ_0001
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:496
[ ERROR ] UtilityExitException
ERROR: Chain '1' is not directly built by any jump.
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: (0) [ WARNING ] ETQ_0001 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy ETQ.pdb
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy ETQ.pdb
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Transform - transform=======================
ERROR: Chain '1' is not directly built by any jump.
ERROR:: Exit from: src/core/pose/chains_util.cc line: 496
protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:496
[ ERROR ] UtilityExitException
ERROR: Chain '1' is not directly built by any jump.
protocols.jd2.JobDistributor: (0) [ ERROR ]
[ERROR] Exception caught by JobDistributor for job ETQ_0002
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:496
[ ERROR ] UtilityExitException
ERROR: Chain '1' is not directly built by any jump.
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: (0) [ WARNING ] ETQ_0002 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy ETQ.pdb
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy ETQ.pdb
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Transform - transform=======================
ERROR: Chain '1' is not directly built by any jump.
ERROR:: Exit from: src/core/pose/chains_util.cc line: 496
protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:496
[ ERROR ] UtilityExitException
ERROR: Chain '1' is not directly built by any jump.
protocols.jd2.JobDistributor: (0) [ ERROR ]
[ERROR] Exception caught by JobDistributor for job ETQ_0003
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:496
[ ERROR ] UtilityExitException
ERROR: Chain '1' is not directly built by any jump.
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: (0) [ WARNING ] ETQ_0003 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy ETQ.pdb
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy ETQ.pdb
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Transform - transform=======================
ERROR: Chain '1' is not directly built by any jump.
ERROR:: Exit from: src/core/pose/chains_util.cc line: 496
protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:496
[ ERROR ] UtilityExitException
ERROR: Chain '1' is not directly built by any jump.
protocols.jd2.JobDistributor: (0) [ ERROR ]
[ERROR] Exception caught by JobDistributor for job ETQ_0004
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:496
[ ERROR ] UtilityExitException
ERROR: Chain '1' is not directly built by any jump.
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: (0) [ WARNING ] ETQ_0004 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy ETQ.pdb
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from saved copy ETQ.pdb
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Transform - transform=======================
ERROR: Chain '1' is not directly built by any jump.
ERROR:: Exit from: src/core/pose/chains_util.cc line: 496
protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:496
[ ERROR ] UtilityExitException
ERROR: Chain '1' is not directly built by any jump.
protocols.jd2.JobDistributor: (0) [ ERROR ]
[ERROR] Exception caught by JobDistributor for job ETQ_0005
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:496
[ ERROR ] UtilityExitException
ERROR: Chain '1' is not directly built by any jump.
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: (0) [ WARNING ] ETQ_0005 reported failure and will NOT retry
protocols.jd2.JobDistributor: (0) no more batches to process...
protocols.jd2.JobDistributor: (0) 10 jobs considered, 10 jobs attempted in 6 seconds
---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
10 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------
| Attachment | Size |
|---|---|
 ROSETTA_CRASH.log | 49.6 KB |
| ETQ_conformers.pdb | 224.81 KB |
The first error message you get ( "chain_id X does not exist") indicates that Rosetta doesn't think you have a ligand in your input PDB (labeled with chain X).
If you look further up in your log, you can see the information about which structures are being loaded:
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: (0) pushed 3PBL_A.pdb nstruct indices 1 - 5
protocols.jd2.PDBJobInputter: (0) pushed ETQ.pdb nstruct indices 1 - 5
This indicates that the 3PBL_A.pdb protein structure and the ETQ.pdb ligand structure are being loaded as separate jobs, instead of being combined into a protein-ligand complex for the same job.
The way that the protein & ligand are combined into a complex in the tutorial is using an extension of the PDB loading code in Rosetta. By default, the -s option of Rosetta will load each PDB passed as a separate job. But if you quote multiple PDBs together in the -s designation, Rosetta will concatenate the PDBs into a single structure:
-s 3PBL_A.pdb ETQ.pdb
Load 3PBL_A and ETQ are loaded as two independent structures.
-s "3PBL_A.pdb ETQ.pdb"
The 3PBL_A and ETQ are both loaded and merged into a single structure which contains both receptor and ligand.
My guess is that there's some issue with your options.txt which means that the two structures are being loaded separately. There's two way of fixing it. The first is to fix the quoting. The second is to manually combine the receptor and ligand into a single PDB and simply load that one file in the -s option.
(Note there are some versions of Rosetta which don't support the quoted pdb-merging approach, though recent ones (like the one you're using) should support it.)
Thanks, it works well!