Reply To: cluster error

[Anonymous]

I split the PDB by PYMOL and it could be displayed by PYMOL and rasmol(I will paste the file in my next thread).

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Here is the log file.

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core.init: command: /soft/rosetta3.1/rosetta_source/bin/cluster.linuxgccrelease @flags-cluster
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1119224093 seed_offset=0 real_seed=-1119224093
core.init.random: RandomGenerator:init: Normal mode, seed=-1119224093 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: -input_score_filter Ignore structures above certain energy
-exclude_res Exclude residue numbers
-radius Cluster radius
-limit_cluster_size Maximal cluster size
-limit_clusters Maximal number of clusters
-limit_total_structures Maximal number of structures in total
-limit_dist_matrix only pre cluster N structures, then redo.
-sort_groups_by_energy Sort clusters by energy.
-remove_highest_energy_member Remove highest energy member of each cluster
-cluster:radius RMSD in Angstrom
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/rosetta3.1/database/pdb_pair_stats_fine
core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA
core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_n
core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_pp
core.io.database: Database file opened: /soft/rosetta3.1/database/Rama_smooth_dyn.dat_ss_6.4
protocols.jobdist.main: PDB Output Mode
protocols.jobdist.JobDistributors: Looking for an available job: 1 1 test_0002.pdb 1
protocols.jobdist.main: Starting ctest_0002_0001 …