As I recall autodock vina is not set up to dock two ligands at once. That might be a better question to ask the autodock listserve.
Regardless, I would recommend docking one compound at a time to generate a reasonable amount of docking poses. >From the first round of docking you could then treat the individual outputs as static structures and dock the second compound to each structure produced from the first round. You could then go through this process in the reverse to determine any overlap. ~JH morning, Everyone, > We are trying to dock two small molecule ligands into a big active site > of the enzyme. We tried to dock two simultaneously using Autodock Vina, > but one always got kicked out. Is there a way we can dock both ligands? > Thanks for your suggestions. > Best, > Haiying >
