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

    Here is the log file.

    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
    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
    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. Database file opened: /soft/rosetta3.1/database/pdb_pair_stats_fine Database file opened: /soft/rosetta3.1/database/P_AA Database file opened: /soft/rosetta3.1/database/P_AA_n Database file opened: /soft/rosetta3.1/database/P_AA_pp 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 …