hi,

From your crystal structure(protein-ligand complex), try to find the residues involved in the interactions with ligand molecule. from this information you can find the residues and then set the grid accordingly.

you can also have a look in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4468813/

I was doing the same, but ı was not sure to do right thing, thank you Muhammed , nasseem. but ı want to ask another question,, for example in usfc chimera we used blind docking and after that we try to find where our ligand bound,, can ı use the same technic? label ligand different color and than using autodock tool to grid,, and note that coordinates?