I want to use AutoDock GPU, which accepts protein.maps.fld and ligand.pdbqt files.

Since I am performing high throughput virtual screening, shall I just load protein AutoDockTools and create protein.maps.fld file, which I can use in my command line run of AutoDock GPU run?

I have 1 million ligands in my screening library, so can't repeat the above procedure on all ligands, or shall I just pick a ligand that contains all types of atoms a ligand can have in that ligand library and produce protein.maps.fld based upon that ligand along with the given protein?



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