Docking programs like AutoDock Vina and Schrödinger’s Glide typically require users to specify a docking box. VMD is a popular program for molecular visualization. I often want to visualize the receptor atoms that fall within a given docking box in VMD. This little app generates the VMD selection of these atoms.
Box center (x,y,z):
Box dimensions (x,y,z):
VMD selection: