Member Site Forums Rosetta 3 Rosetta 3 – General cluster error

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    • #720

        I’ve generated one PDB file containing several strucrues of the same protein MD trjactory by VMD. I try to use the cluster protocol to cluster my structure, but it is always says: the PDB format can not recognize by Rosetta. I also split the one file into different indivisual structural files, but the error is still there.Could you please give me some advices for this issue?
        Thank you very much.

      • #4761

          Post a copy of one of your split PDBs and I’ll see if there’s something wrong it with. Use the file attachment option (should be above “preview” when you post) rather than pasting it into the text window.

          You could also just try comparing it against the official PDB file specification (at the PDB site).

          Do these PDBs load into other programs like pymol or rasmol?

          • #4767

              Here is my PDB file you can find it enclosed thread. And I would be very appreciated if you could give me some advices how to make it to be read by Rosetta during cluster. I generate it by Pymol.

          • #4762

              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 …

            • #4772

                The problem with your PDB file is that all your occupancies are zero (columns 54-59). Change column 56 to be 1 instead of 0 (so the occupancies are all 1.00 instead of 0.00) and it will work fine. Rosetta silently ignores zero-occupancy atoms; for these PDBs it silently ignores the entire PDB and crashes down the line.

                I believe the flag “-trust_missing_coords” will have the same effect if you don’t want to use a script to fix all your PDB files.

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