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
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?
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
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...