protein structure prediction using relax — high-powered jobs

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  • Author
    Posts
    • May 31, 2011 at 1:29 am #923
      Anonymous

        Quick question, I am interested in refining a few homology models with long runs of the relax protocol. I find the run time is fairly short on my local supercomputer system, and I’d like to make maximum use of the resources available to me. So, how do I improve my models by refining for a week instead of just a few minutes without having the job exiting? (Note: I believe the run exits normally.)

        Also, is there a good order to use the applications when it comes to relax / loop modeling / backrub?

        Thanks,

        Rob

        ***

        My command:
        sqsub -q mpi -n 128 -r 7d -o out.log /work/username/rosetta/rosetta_source/bin/relax.mpi.linuxgccrelease @flags

        script:
        repeat 10000000
        ramp_repack_min 0.02 0.01
        ramp_repack_min 0.250 0.01
        ramp_repack_min 0.550 0.01
        ramp_repack_min 1 0.00001
        accept_to_best
        endrepeat

        flags file:
        -relax
        -script script10000000
        -constrain_relax_to_start_coords 1
        -ramp_constraints 1

        -in
        -file
        -s protein.pdb

        -path .
        -database /work/rf/rosetta/rosetta_database

        -out
        -nstruct 1
        -pdb
        -prefix aa
        -file
        -fullatom
        -o relax.fasc
        -mute core.util.prof

      • May 31, 2011 at 2:54 pm #5672
        Anonymous

          The most obvious suggestion is to increase the number of models you generate for each input structure (e.g. by increasing the parameter to -nstruct). Almost all Rosetta protocols are stochastic, so there’s a chance that any given run will get hung up in a local minimum. Typically people will run hundreds to thousands of structures, and then pick the “best” models from the set.

          Aside from that, I’m not sure that performing longer runs would necessarily provide you with any better results. I’m not really a relax user, but it’s my understanding that at a certain point, you basically reach convergence and start “drilling down” in the energy function without much change/improvement to the actual structure. (Keep in mind that the Rosetta energy function isn’t perfect and is rather rugged at fine scales, so those last several energy units 1) might not take you closer to the native structure and 2) might result in structures insignificantly different than those from a shorter run.) Is there some reason to suspect that the output structures are sub-optimal? If so, you might have better results trying other protocols, rather than just a longer relax.

        • May 31, 2011 at 6:04 pm #5673
          Anonymous

            Basically, I am trying to maximize the quality of the model to make one that is suitable as a search model for molecular replacement. I’m not sure if that’s realistic, but the current model I have isn’t working, so I thought I’d give it a try.

            Any ideas regarding the second question as to whether order matters for relax, loop modeling and backrub?

          • June 7, 2011 at 8:11 pm #5727
            Anonymous

              Hi,

              I was just trying out the example from the paper listed above (without including the map just yet) — I keep running into this error:
              protocols.jd2.ThreadingJobInputter: (0) Warning: no template pdb provided for alignment

              My command:

              ~/mr_protocols.linuxgccrelease @flags

              Flags file:
              -database /work/rf/rosetta/rosetta_database
              -MR:mode cm
              -in:file:extended_pose 1
              -in:file:fasta fj6376.fasta
              -in:file:alignment 2h1q.ali
              -in:file:template_pdb 2h1q.pdb

              -loops:frag_sizes 9 3 1
              -loops:frag_files aaFJ63_09_05.200_v1_3.gz aaFJ63_03_05.200_v1_3.gz none
              -loops:random_order
              -loops:random_grow_loops_by 5
              -loops:extended
              -loops:remodel quick_ccd
              -loops:relax relax

              -relax:default_repeats 4
              -relax:jump_move true

              #-edensity:mapreso 1.6
              #-edensity:grid_spacing 1.5
              #-edensity:mapfile target.map
              #-edensity:sliding_window_wt 1.0
              #-edensity:sliding_window 5

              -cm:aln_format grishin
              -MR:max_gaplength_to_model 10
              -nstruct 1

              My directory contents includes 2h1q.pdb

              Also, I tried another case where I just used the words “target” “template” etc… without the specific details and no luck. Am I missing something obvious?

              Thanks.

              ***

              Full output:

              [rf@tig241 test]$ /work/rf/rosetta/rosetta_source/bin/mr_protocols.linuxgccrelease @flags -overwrite true
              core.init: (0) Mini-Rosetta version exported from unknown
              core.init: (0) command: /work/rf/rosetta/rosetta_source/bin/mr_protocols.linuxgccrelease @flags -overwrite true
              core.init: (0) ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=227767109 seed_offset=0 real_seed=227767109
              core.init.random: (0) RandomGenerator:init: Normal mode, seed=227767109 RG_type=mt19937
              core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: standard
              core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
              core.scoring.etable: (0) Starting energy table calculation
              core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well
              core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)
              core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)
              core.scoring.etable: (0) Finished calculating energy tables.
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/pdb_pair_stats_fine
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBEval.csv
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA_n
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA_pp
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/Rama_smooth_dyn.dat_ss_6.4
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/env_log.txt
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/cbeta_den.txt
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/pair_log.txt
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/cenpack_log.txt
              core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: standard
              core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
              protocols.loops.loops_main: (0) Frag libraries debug aaFJ63_09_05.200_v1_3.gz 9
              core.io.fragments: (0) reading fragments from file: aaFJ63_09_05.200_v1_3.gz …
              core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader…
              core.fragments.ConstantLengthFragSet: (0) finished reading top 200 9mer fragments from file aaFJ63_09_05.200_v1_3.gz
              protocols.loops.loops_main: (0) Frag libraries debug aaFJ63_03_05.200_v1_3.gz 3
              core.io.fragments: (0) reading fragments from file: aaFJ63_03_05.200_v1_3.gz …
              core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader…
              core.fragments.ConstantLengthFragSet: (0) finished reading top 200 3mer fragments from file aaFJ63_03_05.200_v1_3.gz
              protocols.loops.loops_main: (0) Frag libraries debug none 1
              protocols.loops.loops_main: (0) Set up 1-mer library from 3-mer library
              protocols.loops.loops_main: (0) Fragment libraries: 1 147600
              protocols.loops.loops_main: (0) Fragment libraries: 3 49200
              protocols.loops.loops_main: (0) Fragment libraries: 9 48000
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE1 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE1 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU 48
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 48
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 48
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 48
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OG1 on residue THR 49
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG2 on residue THR 49
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH1 on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH2 on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLN 56
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLN 56
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLN 56
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE2 on residue GLN 56
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLN 93
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLN 93
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLN 93
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE2 on residue GLN 93
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue ASP 104
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OD1 on residue ASP 104
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OD2 on residue ASP 104
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 131
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 131
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 131
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue LEU 133
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue LEU 133
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue LEU 133
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue ARG 190
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH1 on residue ARG 190
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH2 on residue ARG 190
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 219
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 219
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue LYS 233
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue LYS 233
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 233
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 233
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue LYS 235
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 235
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 235
              core.pack.task: (0) Packer task: initialize from command line()
              core.pack.pack_missing_sidechains: (0) packing residue number 1 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 47 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 48 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 49 because of missing atom number 6 atom name OG1
              core.pack.pack_missing_sidechains: (0) packing residue number 50 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 56 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 93 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 104 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 131 because of missing atom number 7 atom name CD
              core.pack.pack_missing_sidechains: (0) packing residue number 133 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 190 because of missing atom number 9 atom name CZ
              core.pack.pack_missing_sidechains: (0) packing residue number 219 because of missing atom number 8 atom name CE
              core.pack.pack_missing_sidechains: (0) packing residue number 233 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 235 because of missing atom number 7 atom name CD
              core.scoring.dunbrack: (0) Dunbrack library took 0.07 seconds to load from binary
              core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
              core.pack.pack_rotamers: (0) built 145 rotamers at 14 positions.
              core.pack.pack_rotamers: (0) IG: 12300 bytes
              protocols.jd2.ThreadingJobInputter: (0) Warning: no template pdb provided for alignment 2H1Q.PDB
              protocols.jd2.JobDistributor: (0) no more batches to process…
              protocols.jd2.JobDistributor: (0) 0 jobs considered, 0 jobs attempted in 0 seconds
              protocols.jd2.JobDistributor: (0) no jobs were attempted, did you forget to pass -overwrite?
              [rf@tig241 test]$ /work/rf/rosetta/rosetta_source/bin/mr_protocols.mpi.linuxgccrelease @flags -overwrite true
              core.init: (0) Mini-Rosetta version exported from unknown
              core.init: (0) command: /work/rf/rosetta/rosetta_source/bin/mr_protocols.mpi.linuxgccrelease @flags -overwrite true
              core.init: (0) ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1806468607 seed_offset=0 real_seed=1806468607
              core.init.random: (0) RandomGenerator:init: Normal mode, seed=1806468607 RG_type=mt19937
              core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: standard
              core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
              core.scoring.etable: (0) Starting energy table calculation
              core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well
              core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)
              core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)
              core.scoring.etable: (0) Finished calculating energy tables.
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/pdb_pair_stats_fine
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/scoring/score_functions/hbonds/standard_params/HBEval.csv
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA_n
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/P_AA_pp
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/Rama_smooth_dyn.dat_ss_6.4
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/env_log.txt
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/cbeta_den.txt
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/pair_log.txt
              core.io.database: (0) Database file opened: /work/rf/rosetta/rosetta_database/cenpack_log.txt
              core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: standard
              core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION PATCH: score12
              protocols.loops.loops_main: (0) Frag libraries debug aaFJ63_09_05.200_v1_3.gz 9
              core.io.fragments: (0) reading fragments from file: aaFJ63_09_05.200_v1_3.gz …
              core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader…
              core.fragments.ConstantLengthFragSet: (0) finished reading top 200 9mer fragments from file aaFJ63_09_05.200_v1_3.gz
              protocols.loops.loops_main: (0) Frag libraries debug aaFJ63_03_05.200_v1_3.gz 3
              core.io.fragments: (0) reading fragments from file: aaFJ63_03_05.200_v1_3.gz …
              core.io.fragments: (0) rosetta++ fileformat detected! Calling legacy reader…
              core.fragments.ConstantLengthFragSet: (0) finished reading top 200 3mer fragments from file aaFJ63_03_05.200_v1_3.gz
              protocols.loops.loops_main: (0) Frag libraries debug none 1
              protocols.loops.loops_main: (0) Set up 1-mer library from 3-mer library
              protocols.loops.loops_main: (0) Fragment libraries: 1 147600
              protocols.loops.loops_main: (0) Fragment libraries: 3 49200
              protocols.loops.loops_main: (0) Fragment libraries: 9 48000
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE1 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE_p:NtermProteinFull 1
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE1 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE2 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue PHE 47
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLU 48
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 48
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 48
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 48
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OG1 on residue THR 49
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG2 on residue THR 49
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH1 on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH2 on residue ARG 50
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLN 56
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLN 56
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLN 56
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE2 on residue GLN 56
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue GLN 93
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLN 93
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLN 93
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NE2 on residue GLN 93
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue ASP 104
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OD1 on residue ASP 104
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OD2 on residue ASP 104
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue GLU 131
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE1 on residue GLU 131
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OE2 on residue GLU 131
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue LEU 133
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD1 on residue LEU 133
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD2 on residue LEU 133
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CZ on residue ARG 190
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH1 on residue ARG 190
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NH2 on residue ARG 190
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 219
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 219
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CG on residue LYS 233
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue LYS 233
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 233
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 233
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CD on residue LYS 235
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 235
              core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 235
              core.pack.task: (0) Packer task: initialize from command line()
              core.pack.pack_missing_sidechains: (0) packing residue number 1 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 47 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 48 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 49 because of missing atom number 6 atom name OG1
              core.pack.pack_missing_sidechains: (0) packing residue number 50 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 56 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 93 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 104 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 131 because of missing atom number 7 atom name CD
              core.pack.pack_missing_sidechains: (0) packing residue number 133 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 190 because of missing atom number 9 atom name CZ
              core.pack.pack_missing_sidechains: (0) packing residue number 219 because of missing atom number 8 atom name CE
              core.pack.pack_missing_sidechains: (0) packing residue number 233 because of missing atom number 6 atom name CG
              core.pack.pack_missing_sidechains: (0) packing residue number 235 because of missing atom number 7 atom name CD
              core.scoring.dunbrack: (0) Dunbrack library took 0.08 seconds to load from binary
              core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
              core.pack.pack_rotamers: (0) built 145 rotamers at 14 positions.
              core.pack.pack_rotamers: (0) IG: 12300 bytes
              protocols.jd2.ThreadingJobInputter: (0) Warning: no template pdb provided for alignment 2H1Q.PDB
              protocols.jd2.JobDistributor: (0) no more batches to process…
              protocols.jd2.JobDistributor: (0) 0 jobs considered, 0 jobs attempted in 0 seconds
              protocols.jd2.JobDistributor: (0) no jobs were attempted, did you forget to pass -overwrite?

            • June 8, 2011 at 2:35 pm #5729
              Anonymous

                Looking at the code around the error, I think your problem may be in your alignment file. No template PDB at all should spit a critical error (crash) “ThreadingJobInputter needs parent-pdbs either as in:file:template_pdb or as in:file:template_silent “. This error occurs at the end of a search for the appropriate alignment – I guess from that .ali file….? (In case you can’t tell I’ve never used the threading inputter…)

                By the way, the -overwrite suggestion is a red herring; normally if no jobs are completed it’s because someone re-ran a job where the results already existed. so overwrite is suggested. Here, no jobs are created (because of the failure in figuring out alignments with which to create them); no jobs created = no jobs run = overwrite hint.

              • June 8, 2011 at 4:36 pm #5737
                Anonymous

                  My alignment file is in this format.
                  ## FJ637 2h1q.pdb
                  # hhsearch
                  scores_from_program: -999 100.00
                  7 RIKKKAMELA (…) ESESIKYVIE
                  5 EIYDAMINGI (…) YSAGQKVTIK
                  —

                  And, like I say, the 2h1q.pdb is in the directory and when I open it it seems like a very normal file:

                  ATOM 1 N PHE A 1 -0.433 28.290 54.674 1.00 88.88 N
                  (…)
                  ATOM 1867 OXT LYS A 247 0.587 32.549 77.191 1.00 56.78 O
                  TER

                  And, for reference, here’s the fasta file:
                  >NP_143367.1 gi|14591289|ref|NP_143367.1| hypothetical protein [Pyrococcus horikoshii]
                  MNGMLLSRIKKKAMELAEDLKLVDFSFGLPYTWVLVEGIEGRALGVAMTLPEEVQRYTNS
                  IEEPSLLEFIDKADSLNIIERTLGVAAINAVSQYYIDLREAKWIDVTELIQQDEIKRIAI
                  IGNMPPVVRTLKEKYEVYVFERNMKLWDRDTYSDTLEYHILPEVDGIIASASCIVNGTLD
                  MILDRAKKAKLIVITGPTGQLLPEFLKGTKVTHLASMKVTNIEKALVKLKLGSFKGFESE
                  SIKYVIEV

                  If you have any further ideas of how to edit the alignment file, let me know.

                  Thanks!!

                • June 8, 2011 at 7:10 pm #5738
                  Anonymous

                    Hello,

                    Sorry for the slow response to this.

                    Rocco’s comments on sampling are correct. With relax alone, generally more than 5-10 structures are overkill; if you want to best spend large amounts of computer time, then exploring larger conformational changes with looprelax is preferred.

                    Regarding the error, this is a minor bug in the ThreadingJob inputter. If you change the first line of the .ali file to read:
                    ## FJ637 2h1q
                    (dropping the ‘.pdb’) then it should work.

                    -Frank DiMaio

                  • June 1, 2011 at 5:04 pm #5681
                    Anonymous

                      If you’re attempting to use models for molecular replacement, you’ll probably be interested in the following paper:

                      DiMaio et al. “Improved molecular replacement by density- and energy-guided protein structure optimization.” (2011) Nature, doi:10.1038/nature09964

                      My understanding is that, while lower energy structures in the Rosetta energy function were more likely to give good results, having a large diversity of structures and a thoroughly sampled conformational space was also key to finding a good search model. So instead of taking a single structure and really optimizing it with relax, its likely better to create a range of structures, and consider each of them for molecular replacement.

                      For the ordering, you’re probably best served by loop modeling, then backrub, then relax. That is, going from more course, drastic operations to finer, more refinement operations. Loop modeling makes big changes to backbone structure, whereas backrub makes finer, more local changes, and relax is to some extent a final minimization step. Another technique to try is to apply them in cycles to walk from one minima to the other. (Loop modeling moves you to another region of search space, and then backrub and relax reorganizes you around that new conformation, which sets you up to find a different set of conformations in the next round of loop modeling.)

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