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Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)

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Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)
#1
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Dear Friends, 

 

I am running ab initio rosetta run using openmpi:

  

mpiexec -np 16 /main/source/bin/AbinitioRelax.mpi.linuxgccrelease -database /main/database/ @options -mpi_tracer_to_file log > log1.log &

 

I see "score.fsc" file in the folder with 2000 models, and generated a RMSD vs Energy plot, whcih gives me this (the attached plot)

All 2000 models have 0.00 RMSD, is this normal? Do I need to wait for the models to converge? your commensts and solutions are very welcome. thanks

AttachmentSize
RMSD-ENERGY-plot.png28.3 KB
Category: 
Structure prediction
Post Situation: 
Unsolved
Mon, 2019-09-23 03:24
Danielsebas
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Hello,

I cannot be sure without seeing your 'options' file, but it looks like to me you haven't added the flag: 

-in:file:native {my_native_pdb_file}

which gives rosetta a structure to calculate an RMSD against.

if that isn't the case, please paste your options file here!

Mon, 2019-09-23 07:29
danpf
(Reply to #3)
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Thanks! there is no template pdb as it is a de novo structure prediciton. My options file is:

  

# Make sure all variable names have been replaced with absolute path and that no line begins with a $ or ~s
-in
        -file
                -fasta sequence.fasta         # protein sequence in fasta format
                -frag3 t001_.200.3mers  # protein 3-residue fragments file
                -frag9 t001_.200.9mers  # protein 9-residue fragments file
-abinitio
        -relax
        -increase_cycles 10     # Increase the number of cycles at each stage in AbinitioRelax by this factor
        -rg_reweight 0.5        # Reweight contribution of radius of gyration to total score by this scale factor
        -rsd_wt_helix 0.5       # Reweight env, pair, and cb scores for helix residues by this factor
        -rsd_wt_loop 0.5        # Reweight env, pair, and cb scores for loop residues by this factor
-relax
        -fast   # At the end of the de novo protein_folding, do a relax step of type "FastRelax".  This has been shown to be the best deal for speed and robustness.
-out
        -nstruct 50000  # how many structures do you want to generate?  Usually want to fold at least 1,000.
        -file
                -silent abrelax.out # full path to silent file output
                -silent_struct_type binary      # we want binary silent files
                -scorefile score.sc
-overwrite      # overwrite any existing output with the same name you may have generated
-nstruct 50000

Please let me know about your suggestions. Thanks.

Mon, 2019-09-23 07:47
Danielsebas
(Reply to #4)
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Rosetta can't give an RMSD if you don't give it a structure to RMSD against.  RMSD is relevant when you have a "correct structure" to compare to (meaning, for benchmarking purposes).  If you are doing an unknown protein it's not a useful metric here.

After generating models you can do a second-pass re-scoring calculating RMSD against the best model.  If that score versus RMSD plot shows a funnel it's a good sign that the model is correct.

Mon, 2019-09-23 09:24
smlewis
(Reply to #5)
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thanks! Could you please let me know how to do this re-scoring? i am trying to find it in the tutorials but not successfull. thanks

Mon, 2019-09-23 09:43
Danielsebas
(Reply to #6)
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I don't remember, but off the top of my head, just run them all through score_jd2 with -in:file:native set to whichever model you want them compared to.  

Mon, 2019-09-23 11:42
smlewis