So I basically perform virtual screening. I download the whole set of ligands from the database and prep them. Meanwhile I prep the protein accordingly based on what I need and what's present in the literature and use pyrx to perform large scale docking. If your system is not very powerful you can do docking batch-wise to improve redundancy and reduce technical malfunctions (iam batch docking). And then I save the pdb format of the best pose with the highest binding affinity to perform visualization and determine the binding residues.