Hi,

you have two options:

1) use AutoDockTools to visually determine box dimensions (grid size), usually based on previous docking and/or co-crystal ligands;

2) use smina to automatically determine grid box parameters from selected residues;

Hello Zeng,

The binding site of your ligands could be searched in Protein Data Bank (https://www.rcsb.org/) or in the literature. Maybe your molecular targets contain previous experimental evidence published in the literature. In addition, you can take a look at the crystallographic structures of your protein, (or its homologs) complexed with other ligands that act as inhibitors.

The spatial coordinates of the center of the cavity could be determined using some binding site prediction servers. See some examples below:

https://prankweb.cz/

Best wishes,