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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
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:gdtmm Cluster by gdtmm instead of rms
-cluster:input_score_filter
-cluster:exclude_res
-cluster:radius
-cluster:limit_cluster_size
-cluster:limit_clusters
-cluster:limit_total_structures
-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