cluster error

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    • March 6, 2011 at 11:02 am #816
      Anonymous

        Hello:
        I generated several conformation of my protein by CONCOORD and I try to cluster then with Rosetta. However, it doesn’t work:

        core.io.pdb.file_data: [ WARNING ] can’t find atom for res 14 atom ND2 (trying to set temp)
        core.io.pdb.file_data: [ WARNING ] can’t find atom for res 14 atom OD1 (trying to set temp)
        core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CG1 (trying to set temp)
        core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CG2 (trying to set temp)
        core.io.pdb.file_data: [ WARNING ] can’t find atom for res 17 atom CG1 (trying to set temp)
        core.io.pdb.file_data: [ WARNING ] can’t find atom for res 17 atom CG2 (trying to set temp)

        ERROR: Illegal attempt to score with non-identical atom set between pose and etable
        ERROR:: Exit from: src/core/scoring/etable/EtableEnergy.cc line: 80

      • March 6, 2011 at 1:53 pm #5125
        Anonymous

          The error indicates you have a non-matching atom type set and score function. The warnings suggest you probably have full-atom poses that you are trying to read in to a protocol that expects centroid poses (because it is rejecting sidechain heavy atoms). Try a flag to indicate you want full atom poses, like in::file::fullatom, or maybe the other way around, a flag that forces it to convert inputs to centroid?

          Which executeable is this? Are you trying to do fullatom or centroid?

        • March 8, 2011 at 7:24 pm #5136
          Anonymous

            How many structures are you trying to cluster? Does it seem that it gets to the end of the list and crashes, or is it crashing midway through? It could be that one particular structure is bad, or you are running out of memory halfway through.

            You may get more information if you run the code and let it print output to your terminal, instead of using a logfile – this usually doesn’t buffer, so the output won’t end midline like it does now.

            You will get a LOT more information if you compile and run in debug mode (preferably in a debugger) – this will, of course, take probably many hours, and requires knowledge of how to use the debugger…

          • 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

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