I'm wondering if there is a way to constrain the packer based on pairs of residues. As a simple example, say I would like to penalize designs that place an Asn and a Ser at positions i and i+2. In this case, I might think that this would inadvertantly introduce a glycosylation site, and so I'd like to penalize their occurence. I know there are residue type constraints where I can assign a penalty/bonus to individual residue types at a position, but is there a way to set up constraints for pairs of residues at specific positions? This is just a simple example, but I'd rather not just filter out designs.
If I'm unable to set up constraints for the packer, is there a way in rosetta scripts to set up penalties on whole structure energies?
Thanks in advance,