ERROR: Unable to open file: ./1brs_0001.pdb

[Anonymous]

I just install Rosetta 3 and I am trying to run one of the demos to see if the software is installed correctly and to learn how to use Rosetta Dock.

when in directory:

rosetta3_demos/Docking

I issue the command:

../../rosetta3_source/bin/docking_protocol.linuxgccrelease @flags -database ../../rosetta3_database/

and I get the following output:

core.init: command: ../../rosetta3_source/bin/docking_protocol.linuxgccrelease @flags -database ../../rosetta3_database/
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-196952619 seed_offset=0 real_seed=-196952619
core.init.random: RandomGenerator:init: Normal mode, seed=-196952619 RG_type=mt19937
core.io.database: Database file opened: ../../rosetta3_database/env_log.txt
core.io.database: Database file opened: ../../rosetta3_database/cbeta_den.txt
core.io.database: Database file opened: ../../rosetta3_database/pair_log.txt
core.io.database: Database file opened: ../../rosetta3_database/cenpack_log.txt
core.io.database: Database file opened: ../../rosetta3_database/interchain_env_log.txt
core.io.database: Database file opened: ../../rosetta3_database/interchain_pair_log.txt
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.
core.io.database: Database file opened: ../../rosetta3_database/pdb_pair_stats_fine
core.io.database: Database file opened: ../../rosetta3_database/P_AA
core.io.database: Database file opened: ../../rosetta3_database/P_AA_n
core.io.database: Database file opened: ../../rosetta3_database/P_AA_pp
core.init: command: ../../rosetta3_source/bin/docking_protocol.linuxgccrelease @flags -database ../../rosetta3_database/
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-192588239 seed_offset=0 real_seed=-192588239
core.init.random: RandomGenerator:init: Normal mode, seed=-192588239 RG_type=mt19937
protocols.jobdist.JobDistributors: Looking for an available job: 1 1 input/1brs.pdb 1
protocols.jobdist.main: Starting 1brs_0001 …
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 12 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 28 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 101 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 115 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 124 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 161 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 164 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 167 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 176 in file input/1brs.pdb. Best match rsd_type: GLN
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG_p:CtermProteinFull 107
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER_p:CtermProteinFull 193
core.pack.task: Packer task: initialize from command line()
core.io.pdb.file_data: WARNING can’t find atom for res 1 atom H (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 12 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 28 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 101 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 108 atom H (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 115 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 124 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 161 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 164 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 167 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 176 atom 3HG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 12 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 28 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 101 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 115 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 124 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 161 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 164 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 167 in file input/1brs.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 176 in file input/1brs.pdb. Best match rsd_type: GLN
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG_p:CtermProteinFull 107
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER_p:CtermProteinFull 193
core.pack.task: Packer task: initialize from command line()
core.io.pdb.file_data: WARNING can’t find atom for res 1 atom H (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 12 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 28 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 101 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 108 atom H (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 115 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 124 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 161 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 164 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 167 atom 3HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 176 atom 3HG (trying to set temp)
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 107 -1 EDGE 1 108 1 EDGE 108 193 -1
protocols.docking.DockingProtocol:
protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 71 -1 EDGE 71 107 -1 EDGE 71 126 1 EDGE 126 108 -1 EDGE 126 193 -1
protocols.docking.DockingProtocol:
protocols.docking.DockingInitialPerturbation: Reading options…
protocols.docking.DockingInitialPerturbation: randomize1: true
protocols.moves.RigidBodyMover: Randomize: Jump (before): RT 0.519821 0.740403 -0.426132 0.587348 0.0524614 0.807633 0.620329 -0.670112 -0.407604 -6.52363 -0.991516 -22.9906
protocols.moves.RigidBodyMover: Randomize: Rot (before): 20.8207 44.0982 12.3129
protocols.geometry.RB_geometry: random_reorientation_matrix phi: 356.855 psi: 208.941 theta: 49.5384
protocols.moves.RigidBodyMover: Randomize: Jump (after): RT 0.0254278 -0.63849 -0.76921 -0.717147 -0.54772 0.430933 -0.696458 0.540679 -0.471818 -16.3848 11.5622 12.7461
protocols.moves.RigidBodyMover: Randomize: Rot (after): 20.8207 44.0982 12.3129
protocols.moves.RigidBodyMover: Randomize: —
protocols.docking.DockingInitialPerturbation: dock_pert: true
protocols.docking.DockingInitialPerturbation: option[ docking::dock_pert ]()8 3
protocols.docking.DockingInitialPerturbation: axis_spin: true
protocols.moves.RigidBodyMover: Spin: Jump (before): RT -0.181854 -0.529129 -0.828826 -0.660222 -0.558939 0.501692 -0.728722 0.638443 -0.247697 -15.8713 14.0894 13.2615
protocols.moves.RigidBodyMover: Spin: Rot (before: 13.4388 54.7846 -9.64399
protocols.moves.RigidBodyMover: Spin: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -20.6461 11.2245 8.96721
protocols.moves.RigidBodyMover: Spin: Rot (after): 13.4388 54.7846 -9.64399
protocols.moves.RigidBodyMover: Spin: —
core.io.database: Database file opened: ../../rosetta3_database/env_log.txt
core.io.database: Database file opened: ../../rosetta3_database/cbeta_den.txt
core.io.database: Database file opened: ../../rosetta3_database/pair_log.txt
core.io.database: Database file opened: ../../rosetta3_database/cenpack_log.txt
protocols.docking.DockingInitialPerturbation: sliding into contact
protocols.docking.DockingInitialPerturbation: Moving away
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -20.6461 11.2245 8.96721
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -21.3409 11.8499 9.32255
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -21.3409 11.8499 9.32255
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -22.0356 12.4752 9.67788
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -22.0356 12.4752 9.67788
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -22.7304 13.1005 10.0332
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -22.7304 13.1005 10.0332
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -23.4252 13.7259 10.3886
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -23.4252 13.7259 10.3886
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -24.1199 14.3512 10.7439
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -24.1199 14.3512 10.7439
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -24.8147 14.9765 11.0992
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -24.8147 14.9765 11.0992
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -25.5094 15.6019 11.4546
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -25.5094 15.6019 11.4546
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -26.2042 16.2272 11.8099
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -26.2042 16.2272 11.8099
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -26.899 16.8525 12.1653
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -26.899 16.8525 12.1653
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -27.5937 17.4779 12.5206
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -27.5937 17.4779 12.5206
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -28.2885 18.1032 12.8759
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -28.2885 18.1032 12.8759
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -28.9832 18.7285 13.2313
protocols.docking.DockingInitialPerturbation: Moving together
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -28.9832 18.7285 13.2313
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -28.2885 18.1032 12.8759
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -28.2885 18.1032 12.8759
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.576969 -0.782199 -0.235101 0.216309 -0.131231 0.967465 -0.787602 -0.609052 0.0934801 -28.9832 18.7285 13.2313
protocols.docking.DockingProtocol: finished initial perturbation
protocols.TrialMover: Acceptance rate: 0.26
protocols.TrialMover: Acceptance rate: 0.16
protocols.TrialMover: Acceptance rate: 0.08
protocols.TrialMover: Acceptance rate: 0.02
protocols.TrialMover: Acceptance rate: 0.28
protocols.TrialMover: Acceptance rate: 0.1
protocols.TrialMover: Acceptance rate: 0.28
protocols.TrialMover: Acceptance rate: 0.12
protocols.TrialMover: Acceptance rate: 0.3
protocols.TrialMover: Acceptance rate: 0
protocols.docking.DockingLowRes: in DockingLowRes.apply
::::::::::::::::::Centroid Rigid Body Adaptive:::::::::::::::::::
core.scoring.dunbrack: Dunbrack library took 0.05 seconds to load from binary
protocols.docking.DockingProtocol: Doing initial repack of sidechains
core.pack.task: Packer task: initialize from command line()
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 423 rotamers at 52 positions.
core.pack.pack_rotamers: IG: 189008 bytes
protocols.docking.DockingHighRes: in DockingHighRes.apply
core.pack.task: Packer task: initialize from command line()
protocols.docking.DockingHighRes: ::::::::::::::::::DOCK_MCM:::::::::::::::::::
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 129 rotamers at 19 positions.
core.pack.pack_rotamers: IG: 46036 bytes
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 121 rotamers at 19 positions.
core.pack.pack_rotamers: IG: 46748 bytes
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 116 rotamers at 19 positions.
core.pack.pack_rotamers: IG: 45500 bytes
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 115 rotamers at 19 positions.
core.pack.pack_rotamers: IG: 43752 bytes
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 122 rotamers at 19 positions.
core.pack.pack_rotamers: IG: 48216 bytes
protocols.jobdist.main: Finished 1brs_0001 in 23 seconds.

ERROR: Unable to open file: ./1brs_0001.pdb

ERROR:: Exit from: src/protocols/jobdist/JobDistributors.hh line: 978

the file 1brs_0001.pdb does not exist in this directory.

Does anyone have an idea on how to proceed?

Thank you.

Don

[Anonymous]

The log file appears to indicate that Rosetta is running just fine. I think this is a file permission problem. Do you have write permission in the directory that you are attempting to run Rosetta? I can duplicate this error by running Rosetta in a directory for which I do not have write permission.

[Author]

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