I am trying to conduct docking of couple of ligands on a protein using Glide and Autodock vina.
When I want to choose the same grid box using the co-crystalized ligand and protein with the 2 tools, I realize that glide and ADTvina give different Grid x,y,z center coordinates!! is that normal??
Since I want to do the docking with 2 tools and then choose the docked poses that are common between the two, I think it is better to set the same grid box size and coordinates. Or that is not really the case and I just need to chose the grid for each of the tools that gives the lowest re-docked pose RMSD compared to reference?