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
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.