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
I cannot be sure without seeing your 'options' file, but it looks like to me you haven't added the flag:
which gives rosetta a structure to calculate an RMSD against.
if that isn't the case, please paste your options file here!
Thanks! there is no template pdb as it is a de novo structure prediciton. My options file is:
Please let me know about your suggestions. Thanks.
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.
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
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.