Is Snugdock essentially the same as running Docking with an ensemble of conformations generated by Relax?
Not quite. SnugDock is specific to antibody--antigen complexes and builds on the docking protocol to include CDR H2/H3 loop refinement steps. Comparing SnugDock to docking with ensembles, the H2/H3 motions will be larger than those in a relaxed ensemble, while there would be no motion elsewhere. The best approach is to run SnugDock with ensembles, if you are docking an antibody-antigen complex.