Loopmodel with DNA has no energy score

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    • #2194
      Anonymous

        Hi,everyone,recently I’m building a loop with DNA as the geometric restraint. I gave an initial conformation to Rosetta and my command is like this :
        mpirun -np 4 /usr/local/rosetta/rosetta-3.5/rosetta_source/bin/loopmodel.mpi.linuxgccrelease -database /usr/local/rosetta/rosetta-3.5/rosetta_database -loops:remodel perturb_kic -loops:refine refine_kic -in:file:s Loop_v2_withDNA.pdb -in:file:fullatom 1 -loops:fix_natsc 1 -loops:loop_file loopfile -relax:constrain_relax_to_start_coords -relax:coord_ constrain_sidechains -relax:ramp_constraints false -nstruct 500 -ex1 -ex2 -overwrite -no_binary_dunlib 1 -in:::file:native Loop_v2_withDNA.pdb -use_input_sc -flip_HNQ -no_optH false

        When I check the score.sc file , it looked like this :

        1 SEQUENCE:
        2 SCORE: total_score chainbreak dslf_ca_dih dslf_cs_ang dslf_ss_dih dslf_ss_dst fa_atr fa_dun fa_intra_rep fa_pair fa_rep fa_sol hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb loop_cenrms loop_rms omeg a p_aa_pp pro_close rama ref total_energy description
        3 SCORE: 786.306 0.000 0.000 0.000 0.000 0.000 -1197.292 435.428 4.970 -21.481 1076.121 638.798 -26.720 -47.433 -14.554 -52.551 15.205 17.127 49.29 1 -16.280 6.950 -0.621 -48.320 786.306 Loop_v2_withDNA_0001
        4 SCORE: 0.000 Loop_v2_withDNA_0001
        5 SCORE: 0.000 Loop_v2_withDNA_0001
        6 SCORE: 0.000 Loop_v2_withDNA_0001
        7 SCORE: 0.000 Loop_v2_withDNA_0002
        8 SCORE: 793.992 0.000 0.000 0.000 0.000 -1197.317 444.115 10.010 -23.437 1091.526 647.323 -27.804 -46.333 -14.079 -52.186 21.215 -17.422 7.095 -0.394 -48.320 Loop_v2_withDNA_0002
        9 SCORE: 0.000 Loop_v2_withDNA_0002
        10 SCORE: 0.000 Loop_v2_withDNA_0002
        11 SCORE: 0.000 Loop_v2_withDNA_0003
        12 SCORE: 0.000 Loop_v2_withDNA_0003
        13 SCORE: 0.000 Loop_v2_withDNA_0003
        14 SCORE: 0.000 Loop_v2_withDNA_0003
        15 SCORE: 0.000 Loop_v2_withDNA_0004
        16 SCORE: 0.000 Loop_v2_withDNA_0004
        17 SCORE: 0.000 Loop_v2_withDNA_0004
        18 SCORE: 0.000 Loop_v2_withDNA_0004
        19 SCORE: 0.000 Loop_v2_withDNA_0005
        20 SCORE: 0.000 Loop_v2_withDNA_0005
        21 SCORE: 642.502 0.000 0.000 0.000 0.000 -1200.157 422.835 4.514 -23.999 933.315 651.803 -30.558 -46.067 -16.225 -52.126 21.674 -16.055 40.075 1.791 -48.320 Loop_v2_withDNA_0006
        22 SCORE: 0.000 Loop_v2_withDNA_0005

        It gave me nothing about the energy. when I check specific model, I found things were like this:
        2722 ATOM 2722 C4 C 308 41.137 33.106 70.463 1.00 0.00
        2723 ATOM 2723 N4 C 308 42.352 32.865 69.965 1.00 0.00
        2724 ATOM 2724 C5 C 308 40.998 33.654 71.774 1.00 0.00
        2725 ATOM 2725 C6 C 308 39.756 33.846 72.236 1.00 0.00
        2726 ATOM 2726 1H5* C 308 35.404 36.804 74.558 1.00 0.00
        2727 ATOM 2727 2H5* C 308 36.361 37.361 73.180 1.00 0.00
        2728 ATOM 2728 H4* C 308 35.063 35.233 72.914 1.00 0.00
        2729 ATOM 2729 H3* C 308 36.911 34.194 75.044 1.00 0.00
        2730 ATOM 2730 1H2* C 308 36.888 32.010 73.371 1.00 0.00
        2731 ATOM 2731 2H2* C 308 38.125 33.120 73.977 1.00 0.00
        2732 ATOM 2732 H1* C 308 36.592 33.187 71.360 1.00 0.00
        2733 ATOM 2733 1H4 C 308 43.166 33.073 70.508 1.00 0.00
        2734 ATOM 2734 2H4 C 308 42.449 32.476 69.049 1.00 0.00
        2735 ATOM 2735 H5 C 308 41.878 33.909 72.383 1.00 0.00
        2736 ATOM 2736 H6 C 308 39.612 34.267 73.242 1.00 0.00
        2737 TER
        2738 # All scores below are weighted scores, not raw scores.
        2739 #BEGIN_POSE_ENERGIES_TABLE Loop_v2_withDNA_0001.pdb
        2740 label total
        2741 weights NA
        2742 pose#END_POSE_ENERGIES_TABLE Loop_v2_withDNA_0001.pdb

        I found there is no weight for the energy items. I don’t know where went wrong because when I performed the same command to loop modeling without DNA, it worked just fine. I’m quite new to rosetta, can anyone give me some tips or suggestions ?

        Thank you very much

        Yours sincerely

        Nicky

      • #11021
        Anonymous

          It sounds like there’s some error in processing the structures, but one which is intermittent, as you seem to get some structures with reasonable energies. What does the tracer output look like? Are you getting any warning or error messages for the structures which are failing?

          Also, it looks like the loopmodel application may not be working too well with MPI for some reason – it looks like each processor is running on each structure, as opposed to splitting the structures between processors. This means you get four Loop_v2_withDNA_0001 outputs, only the last of which are going to be present on your harddrive, the previous three having been overwritten. Although https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d8/df1/loopmodel.html indicates that if you have the correctly named output directories, this shouldn’t be a problem. I’d check to make sure you’re not wasting time on models you’re always going to ignore, though.

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