Why is AutoDock vina setting the grid center to (0,0,0), and how can I correctly align the grid box with the ligand’s binding site?

In AutoDock, when I drag and drop the PDB file, the binding pocket appears correctly (which I also, confirm by PyMOL and Discovery Studio), but the grid box center (X, Y, Z) is set to (0.0, 0.0,...

21 March 2025 4,486 1 View