I have a question regarding results after water refinement performed using Multi-body interface of Haddock2.2 and the following recipe: Advanced refinement of molecular complexes – Bonvin Lab
I was introducing single mutations into an initial structure of a trimeric protein one by one and then comparing the refined variants according to the resulting energetic scores. Many of the mutated residues are located further than 5 Å from the chain interfaces. And here are my questions:
As I understand now, by default only the interchain energetics are calculated, (including only the residues 5 Å around the interfaces) and therefore the resulting score includes only the energetic contribution of those residues. Is this correct and if not, then contribution of all residues is included?
If the first assumption is right and only energetic contribution of the residues from the interface are included into the final score, then the score of the introduced mutation of a residue beyond 5 Å of the interface is not influenced by the mutation?
Thank you for your time.