Reply To: cluster error

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March 7, 2011 at 8:34 pm #5130
Anonymous

    Thanks a lot for kind rely. I use -fullatom in flag file, but it is doesn’t work, it is said: Segmentation fault

    AND HERE IS THE LOG FILE:
    core.init: Mini-Rosetta version exported from unknown
    core.init: command: cluster.linuxgccrelease @flags
    core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=438295147 seed_offset=0 real_seed=438295147
    core.init.random: RandomGenerator:init: Normal mode, seed=438295147 RG_type=mt19937

    Rosetta Tool: cluster – clustering tool for PDBs and or silent files
    Usage:
    PDB input: -in:file:s *.pdb or
    -in:file:l list_of_pdbs
    -no_optH Dont change positions of Hydrogen atoms!
    Silent input: -in:file:silent silent.out silent input filesname
    -in:file:s specify specific tags to be extracted, if left out all will be taken
    -in:file:fullatom for full atom structures
    -in:file:silent_struct_type specify the input silent-file format
    Native: -in:file:native native PDB if CaRMS is required
    Scorefunction: -score:weights weights weight set or weights file
    -score:patch patch patch set
    -rescore:verbose display score breakdown
    -rescore:output_only don’t rescore
    Output: -nooutput don’t print PDB structures
    -out:prefix myprefix prefix the output structures with a string
    Clustering: -cluster:radius Cluster radius in A (for RMS clustering) or in inverse GDT_TS for GDT clustering. Use “-1” to trigger automatic radius detection
    -cluster:gdtmm Cluster by gdtmm instead of rms
    -cluster:input_score_filter     Ignore structures above certain energy
    -cluster:exclude_res [ ..] Exclude residue numbers
    -cluster:radius Cluster radius
    -cluster:limit_cluster_size Maximal cluster size
    -cluster:limit_clusters     Maximal number of clusters
    -cluster:limit_total_structures     Maximal number of structures in total
    -cluster:sort_groups_by_energy Sort clusters by energy.
    -cluster:remove_highest_energy_member Remove highest energy member of each cluster
    -symmetry:symmetric_rmsd For symmetric systems find the lowest rms by testing all chain combinations. Works only with silent file input that contain symmetry info and with all CA rmsd
    Examples:
    cluster -database ~/minirosetta_database -in:file:silent silent.out -in::file::binary_silentfile -in::file::fullatom -native 1a19.pdb
    clustered Poses are given output names in the form of:
    c.i.j, which denotes the jth member of the ith cluster.

    core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
    core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
    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: /soft/rosetta-3.2/database/pdb_pair_stats_fine
    core.io.database: Database file opened: /soft/rosetta-3.2/database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
    core.io.database: Database file opened: /soft/rosetta-3.2/database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
    core.io.database: Database file opened: /soft/rosetta-3.2/database/scoring/score_functions/hbonds/standard_params/HBEval.csv
    core.io.database: Database file opened: /soft/rosetta-3.2/database/P_AA
    core.io.database: Database file opened: /soft/rosetta-3.2/database/P_AA_n
    core.io.database: Database file opened: /soft/rosetta-3.2/database/P_AA_pp
    core.io.database: Database file opened: /soft/rosetta-3.2/database/Rama_smooth_dyn.dat_ss_6.4
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    core.scoring.dunbrack: Dunbrack library took 0.02 seconds to load from binary
    protocols.cluster: RESCORING: disco_state001.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state002.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state003.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state004.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state005.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state006.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state007.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state008.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state009.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state010.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state011.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state012.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state013.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state014.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state015.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state016.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state017.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state018.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state019.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state020.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state021.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state022.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state023.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state024.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state025.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state026.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state027.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state028.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state029.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state030.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state031.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state032.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state033.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state034.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state035.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state036.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state037.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state038.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state039.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state040.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL_p:CtermProteinFull 17
    core.pack.task: Packer task: initialize from command line()
    protocols.cluster: RESCORING: disco_state041.pdb_loop
    protocols.cluster: Adding struc: 6.95334e-310
    core.conformation.Conformation: [ W