This code is intended to carry out fixed backbone design of RNA sequences given an input backbone.

This demo redesigns a 'UUCG' tetraloop on a single-base pair RNA 'helix', as a small 6-nucleotide test case. As illustration, only 3 designs are output. It takes about 15 seconds to run. Run:

  rna_design.linuxgccrelease @flags -database <PATH TO ROSETTA DATABASE>

The output will show up in:

 chunk001_uucg_RNA.pack.txt 

with scores in

 chunk001_uucg_RNA.pack.out

and PDBs in S_0001.pdb, S_0002.pdb, etc.  
The typical sequence output is cuuggg (native is cuucgg).