We want to dock 2 proteins (red and green) to see how they dimerize. Each crystal structure has 2 parts that are not connected to one another (The receptor at the top and the SKP part below do not have any linkers to make the 2 parts become one chain) They just interact with some electrostatic interactions. This makes the receptor and SKP apart from each other for all docking outputs. From the literature review, we could not reject the SKP part on docking because it has some effect on receptor conformation. How can we constrain this docking problem, since we know some of the interacting residues?
PS. I have tried to get the receptor and SKP on the same chain but the structure was broken. I have also tried to specify the relative chain partners as "AC_BD" (set both SKP parts to be rigid, and receptors to be flexible), but it did not work.