I'm new to Rosetta, and trying to figure out how to calculate the ddG of the interaction between Chain A and Chain B (which homodimerize) for all possible substitutions at each residue compared to wild-type (where Chain A and B will always carry the same mutation). Are there any existing packages that will handle this, or what script would you recommend for my situation?
I'd first recommend reading Kellogg et al. (https://www.ncbi.nlm.nih.gov/pubmed/21287615), which is somewhat of the base reference for dG calculations in Rosetta. You may also want to take a look at https://www.biorxiv.org/content/early/2017/11/17/221689
The Kellogg protocol will probably do what you want, the only limitation being that it's not currently set up for symmetric proteins. You can probably get away with setting up a mutation file which always mutates a pair of corresponding residues. It won't be truely symmetric, in that each monomer can move independent of each other, but it will, at least, set things up to preserve sequence symmetry.