When setting up grids in Glide, what does the purple box enclosing a portion of my structure represent?
The purple box is called the Enclosing box. The volume it encloses represents both the volume within which the grid is computed, and the physical space in which the ligand atoms must remain during docking. It is possible that during docking calculations, a ligand will be too large to fit in the Enclosing box. If a ligand that is too large is discovered during a job, the algorithms will exclude that ligand. New, larger grids must be defined in order to successfully dock such ligands.
