I would like to set up a multidomain flexible docking simulation as desrcibed in Karaca, E. & Bonvin, A. M. J. J. A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes. Structure, 19, 555–565 (2011). I can follow the set up protocol described in the paper on the webserver (i.e., keeping the proper termini neutral, making the bridging residues flexible, using center of mass restraint) with the exception of the connectivity restraints between two domains for it0/it1 versus final refinement (Fig. 2 in the paper). My question is how do I add the second 1.3 A distance restraint during the final refinement?
Thanks is advance your your help!