I am docking a polysaccharide onto a trimeric protein structure. I have merged the trimer into a single chain (e.g. promoter 1 - res 1-130; proteome 2 - res 201-330, etc) and the ligand is docked across two of the promoters. However, after the HADDOCK refinement of the docked complex the relative orientation the trimer chains has changed. Based on subsequent MD simulations this does not appear correct and the original trimer orientation is re-established, which results in half of the polysaccharide being displaced. Is there a way to either still use the trimer within one chain ID or to use the trimer with different chain IDs, but fix their relative orientations.
Many thanks for any help