pepspec aplication – segmentation fault

[Anonymous]

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/rosetta_source
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

[Anonymous]

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.

[Anonymous]

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).

[Anonymous]

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

[Anonymous]

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.

[Author]

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