Hi, I have been using the ddG_RNA tool within ROSIE to calculate relative affinities for my protein and a list of mutant RNAs. Included in the text file list is the WT sequence that is also specified in the PDB file. Based on how I understand the tool works, the ddG bind score for this RNA should be 0, since the value is relative to the WT sequence. Instead I get a score of 3.36. Any idea on why this would be happening?
I am using RNAfold to calculate the mfes for the list of mutant sequences, is it possible that I need to set different folding parameters?