Dear,

I believe the easiest way is to use the autodock tools to create the protein-ligand complex as a pdb file. Then, do the steps to convert the pdb as an amber readable file

Open the dlg file in Autodock and select —Analyze - > conformation - > play, rank by energy.

Conformation window will display the binding energy , ligand efficiency etc.,,, Select the complex with low binding energy and select "Write complex" (.pdb format)....you can visualize the final complex pdb file in any visualization tool (Discovery Studio) ....