Hi,
Running pepspec application, in rosetta 3.3 (mac osx 10.6.7), gives me a segmentation fault. Any idea why this happens?
thank you
Tiago
Log:
core.init: command: ../../rosetta_source/bin/pepspec_anchor_dock.macosgccrelease -database /Users/tiago/software/rosetta/rosetta3.3/rosetta_database/ @dock.args
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1393114305 seed_offset=0 real_seed=1393114305
core.init.random: RandomGenerator:init: Normal mode, seed=1393114305 RG_type=mt19937
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4218 residue types
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 1 in file 1CKA.align.nopep.pdb. Best match rsd_type: ALA_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 5 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 11 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 13 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 21 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 22 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 27 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 29 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 31 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 35 in file 1CKA.align.nopep.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 38 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 45 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 46 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 56 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue TYR_p:CtermProteinFull 57
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TYR_p:CtermProteinFull 57
core.pack.task: Packer task: initialize from command line()
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: pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
basic.io.database: Database file opened: env_log.txt
basic.io.database: Database file opened: cbeta_den.txt
basic.io.database: Database file opened: pair_log.txt
basic.io.database: Database file opened: cenpack_log.txt
basic.io.database: Database file opened: env_log.txt
basic.io.database: Database file opened: cbeta_den.txt
basic.io.database: Database file opened: pair_log.txt
basic.io.database: Database file opened: cenpack_log.txt
basic.io.database: Database file opened: CEN6_mem_env_log.txt
basic.io.database: Database file opened: CEN10_mem_env_log.txt
basic.io.database: Database file opened: memcbeta_den.txt
basic.io.database: Database file opened: mem_pair_log.txt
basic.io.database: Database file opened: P_AA
basic.io.database: Database file opened: P_AA_n
basic.io.database: Database file opened: P_AA_pp
core.scoring.etable: Using alternate parameters: LJ_RADIUS_SOFT in Etable construction.
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.
apps.pilot.chrisk/pep_prep: Initializing prep_1.pdb with 1CKA.align.nopep.pdb
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 1 in file 1CKA.align.nopep.pdb. Best match rsd_type: ALA_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 5 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 11 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 13 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 21 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 22 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 27 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 29 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 31 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 35 in file 1CKA.align.nopep.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 38 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 45 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 46 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 56 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue TYR_p:CtermProteinFull 57
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TYR_p:CtermProteinFull 57
core.pack.task: Packer task: initialize from command line()
core.pack.dunbrack: Dunbrack library took 0.046572 seconds to load from binary
apps.pilot.chrisk/pep_prep: Loading 1N5Z.align.pdb: pep anchor @ chain P seqpos 5
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS_p:CtermProteinFull 71
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TRP_p:CtermProteinFull 81
core.pack.task: Packer task: initialize from command line()
core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 7 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 30 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 55 because of missing atom number 6 atom name CG
basic.io.database: Database file opened: Rama_smooth_dyn.dat_ss_6.4
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 49 rotamers at 4 positions.
core.pack.pack_rotamers: IG: 1908 bytes
apps.pilot.chrisk/pep_prep: RB translation: x, y, z: -20.4696, 6.91372, 4.78153
apps.pilot.chrisk/pep_prep: RB rotation: bond, tor1, tor2: 167.415, 53.9831, 12.4097
apps.pilot.chrisk/pep_prep: Loading 1OEB.align.pdb: pep anchor @ chain D seqpos 3
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER_p:CtermProteinFull 4
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PRO_p:CtermProteinFull 59
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU_p:CtermProteinFull 71
core.pack.task: Packer task: initialize from command line()
apps.pilot.chrisk/pep_prep: RB translation: x, y, z: -20.3002, 6.06507, 5.87712
apps.pilot.chrisk/pep_prep: RB rotation: bond, tor1, tor2: 148.813, 22.7293, 65.6929
apps.pilot.chrisk/pep_prep: Loading 1CKB.align.pdb: pep anchor @ chain B seqpos 2
core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue TYR_p:CtermProteinFull 57
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TYR_p:CtermProteinFull 57
core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG_p:CtermProteinFull 65
core.pack.task: Packer task: initialize from command line()
core.pack.pack_missing_sidechains: packing residue number 65 because of missing atom number 7 atom name CG
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 28 rotamers at 1 positions.
core.pack.pack_rotamers: IG: 900 bytes
apps.pilot.chrisk/pep_prep: RB translation: x, y, z: -20.6863, 6.57256, 4.49366
apps.pilot.chrisk/pep_prep: RB rotation: bond, tor1, tor2: 147.516, 53.4589, 11.0017
apps.pilot.chrisk/pep_prep: peptide stub atoms: CB CA N
RB translation avg: x, y, z: -20.4854, 6.51712, 5.05077
apps.pilot.chrisk/pep_prep: Max RB translation deviation: x, y, z: 0.158029, 0.348669, 0.596018
apps.pilot.chrisk/pep_prep: RB rotation avg: jump_bond_angle, jump_tor1, jump_tor2: 154.581, 43.3904, 29.7014
apps.pilot.chrisk/pep_prep: Max RB rotation deviation: jump_bond_angle, jump_tor1, jump_tor2: 9.09008, 14.6112, 25.4563
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 118 rotamers at 19 positions.
core.pack.pack_rotamers: IG: 52272 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 119 rotamers at 19 positions.
core.pack.pack_rotamers: IG: 54532 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51128 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51128 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 125 rotamers at 20 positions.
core.pack.pack_rotamers: IG: 62524 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
apps.pilot.chrisk/pep_prep: Ignoring clash residues:
Initializing prep_2.pdb with 1CKA.align.nopep.pdb
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 1 in file 1CKA.align.nopep.pdb. Best match rsd_type: ALA_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 5 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 11 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 13 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 21 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 22 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 27 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 29 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 31 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 35 in file 1CKA.align.nopep.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 38 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 45 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 46 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 56 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue TYR_p:CtermProteinFull 57
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TYR_p:CtermProteinFull 57
core.pack.task: Packer task: initialize from command line()
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS_p:CtermProteinFull 71
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TRP_p:CtermProteinFull 81
core.pack.task: Packer task: initialize from command line()
core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 7 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 30 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 55 because of missing atom number 6 atom name CG
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 49 rotamers at 4 positions.
core.pack.pack_rotamers: IG: 1908 bytes
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER_p:CtermProteinFull 4
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PRO_p:CtermProteinFull 59
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU_p:CtermProteinFull 71
core.pack.task: Packer task: initialize from command line()
core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue TYR_p:CtermProteinFull 57
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TYR_p:CtermProteinFull 57
core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG_p:CtermProteinFull 65
core.pack.task: Packer task: initialize from command line()
core.pack.pack_missing_sidechains: packing residue number 65 because of missing atom number 7 atom name CG
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 28 rotamers at 1 positions.
core.pack.pack_rotamers: IG: 900 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 113 rotamers at 17 positions.
core.pack.pack_rotamers: IG: 47420 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 113 rotamers at 17 positions.
core.pack.pack_rotamers: IG: 47420 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51128 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 120 rotamers at 19 positions.
core.pack.pack_rotamers: IG: 55668 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
apps.pilot.chrisk/pep_prep: peptide stub atoms: CB CA N
Ignoring clash residues: 53,
Initializing prep_3.pdb with 1CKA.align.nopep.pdb
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 1 in file 1CKA.align.nopep.pdb. Best match rsd_type: ALA_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 5 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 11 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 13 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 21 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 22 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 27 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 29 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 31 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 35 in file 1CKA.align.nopep.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 38 in file 1CKA.align.nopep.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 45 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 46 in file 1CKA.align.nopep.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 56 in file 1CKA.align.nopep.pdb. Best match rsd_type: LYS
core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue TYR_p:CtermProteinFull 57
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TYR_p:CtermProteinFull 57
core.pack.task: Packer task: initialize from command line()
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 30
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 55
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS_p:CtermProteinFull 71
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TRP_p:CtermProteinFull 81
core.pack.task: Packer task: initialize from command line()
core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 7 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 30 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 55 because of missing atom number 6 atom name CG
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 49 rotamers at 4 positions.
core.pack.pack_rotamers: IG: 1908 bytes
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue SER_p:CtermProteinFull 4
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PRO_p:CtermProteinFull 59
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU_p:CtermProteinFull 71
core.pack.task: Packer task: initialize from command line()
core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue TYR_p:CtermProteinFull 57
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TYR_p:CtermProteinFull 57
core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG_p:CtermProteinFull 65
core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG_p:CtermProteinFull 65
core.pack.task: Packer task: initialize from command line()
core.pack.pack_missing_sidechains: packing residue number 65 because of missing atom number 7 atom name CG
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 28 rotamers at 1 positions.
core.pack.pack_rotamers: IG: 900 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 113 rotamers at 17 positions.
core.pack.pack_rotamers: IG: 47420 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 113 rotamers at 17 positions.
core.pack.pack_rotamers: IG: 47420 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 117 rotamers at 18 positions.
core.pack.pack_rotamers: IG: 51552 bytes
apps.pilot.chrisk/pep_prep: peptide stub atoms: CB CA N
Ignoring clash residues:
bash-3.2$ ../../rosetta_source/bin/pepspec.macosgccrelease -database /Users/tiago/software/rosetta/rosetta3.3/rosetta_database/ @spec.argscore.init: Mini-Rosetta version Release 3.3, from SVN 42942 from https://svn.rosettacommons.org/source/branches/releases/rosetta-3.3/rose...
core.init: command: ../../rosetta_source/bin/pepspec.macosgccrelease -database /Users/tiago/software/rosetta/rosetta3.3/rosetta_database/ @spec.args
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=109059990 seed_offset=0 real_seed=109059990
core.init.random: RandomGenerator:init: Normal mode, seed=109059990 RG_type=mt19937
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: pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
basic.io.database: Database file opened: env_log.txt
basic.io.database: Database file opened: cbeta_den.txt
basic.io.database: Database file opened: pair_log.txt
basic.io.database: Database file opened: cenpack_log.txt
basic.io.database: Database file opened: env_log.txt
basic.io.database: Database file opened: cbeta_den.txt
basic.io.database: Database file opened: pair_log.txt
basic.io.database: Database file opened: cenpack_log.txt
basic.io.database: Database file opened: CEN6_mem_env_log.txt
basic.io.database: Database file opened: CEN10_mem_env_log.txt
basic.io.database: Database file opened: memcbeta_den.txt
basic.io.database: Database file opened: mem_pair_log.txt
basic.io.database: Database file opened: P_AA
basic.io.database: Database file opened: P_AA_n
basic.io.database: Database file opened: P_AA_pp
core.scoring.etable: Using alternate parameters: LJ_RADIUS_SOFT in Etable construction.
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.
apps.public.pepspec: Initializing 1cka_spec_1 with 1cka.docked_2.pdb
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4218 residue types
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PRO_p:CtermProteinFull_p:NtermProteinFull 58
core.pack.task: Packer task: initialize from command line()
apps.public.pepspec: FOLD_TREE EDGE 1 57 -1 JEDGE 1 58 1 CA CB END
apps.public.pepspec:
core.pack.dunbrack: Dunbrack library took 0.0422 seconds to load from binary
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 528 rotamers at 57 positions.
core.pack.pack_rotamers: IG: 343260 bytes
core.fragment.picking_old.vall.vall_io: Reading Vall library from /Users/tiago/software/rosetta/rosetta3.3/rosetta_database/filtered.vall.dat.2006-05-05 ...
core.fragment.picking_old.vall.vall_io: 100000
core.fragment.picking_old.vall.vall_io: 200000
core.fragment.picking_old.vall.vall_io: 300000
core.fragment.picking_old.vall.vall_io: 400000
core.fragment.picking_old.vall.vall_io: 500000
core.fragment.picking_old.vall.vall_io: 600000
core.fragment.picking_old.vall.vall_io: 700000
core.fragment.picking_old.vall.vall_io: 800000
core.fragment.picking_old.vall.vall_io: 900000
Segmentation fault
Rosetta shouldn't segfault (that's the ideal, not the reality). The fact that you're getting one is a sign that something is terribly wrong.
The only real way to debug this is if you compile Rosetta in debug mode. To do this, simply remove the "mode=release" from the compile command. (i.e. run "scons bin" in rosetta/rosetta_source/ ). Debug mode has additional checks which should hopefully tell us where the program is encountering the error. Just running pepspec_anchor_dock.macosgccdebug instead of pepspec_anchor_dock.macosgccrelease *might* be enough, but if you can run it under a debugger (such as gdb) and provide a backtrace, that would be even more informative.
This is a known error - the vall that shipped with 3.3 is broken. Download the rosetta 3.2 database and use the vall file from that (filtered.vall.dat.2006-05-05.gz) until the 3.3 database is repaired. (The file that is being read in during fragment generation, where your crash is, is the vall file).
It worked. Thank you. One other question. I have a macpro with 8 processors. How can i make faster calculations for the pepspec application? Several instance of the executable with different seeds or executing the application with some mpi/jd2 executable?
thank you,
tiago
Multiple instances of the executable, in separate directories, with different seeds, will be the fastest. MPI+JD2 will be nearly as fast if you use the -mpi_work_partition_job_distributor flag (I may have spelled that wrong), and 7/8ths as fast if you use the default MPI+JD2 (the "work pool" implementation, which uses one processor as a head node). (sorry for the delay in answering a simple question, I am digging out from under a lot of stuff...)
I'm not sure pepspec is jd2 (I'm pretty sure it's not), in which case it may be that your only option is the first one.