RNA should be read in correctly from PDBs with no additional input or changes thanks to Rhiju Das. Talaris2013 Scorefunction can score poses with RNA, however relaxation or minimization may need scorefunctions or additional scoreterms which account for delocalized p-orbital ring electrons - aka pi stacking, cation-pi interactions, etc. See this page for more info.


There are many RNA-specific applications within the Rosetta software suite. Please see the rna-applications page and the RNA & RNA-proteins sub-list in applications for more info.