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

Question

I am running rosetta ab initio prediction using the command line:

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

"Options" file looks like this: https://ibb.co/V9VrQHV

RMSD vs Energy plot is: https://ibb.co/1mjzwDj

There is no native structure as this is an ab initio prediction. Could you please let me know about your comments on the RMSD being 0.00 for all 2000 models generated till now? Is this normal and will produce results after more runs?

Answer 1

RMSD is a measure of similarity between two structures. The relevant RMSD in protein structure prediction is between a model and the native structure. If you don't have a native structure you cannot have an RMSD in this sense. Ignore the fact it is 0.0, there is possibly some error that means you are calculating the RMSD between a model and itself.

And that's the difficulty of protein structure prediction... you don't know whether you are right or not! The structures you have generated are your results, and you'll need to find ways to filter or use them that are not reliant on RMSD. You could use estimation of model accuracy methods or clustering, for example.