I'm impressed with Rosetta for the generation of small RNA structures (nt ~ 20) using rna_denovo in combination with the -params_file and -minimize_rna options. When performing a number of runs to select the best scoring one I've noticed there's a correlation between the score of the unminimized structures and the scores after optimization. To speed things up I would like to first generate a larger number of unminimized structures and from this set pick the best scoring ones for further optimization. I'v tried this using rna_minimize but this doesn't seem to work: the resulting scores are much higher than what I get in a run with the minimize_rna flag. Am I missing something here?
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rna_denovo and minize_rna