I use autodock vina for docking. My problem is how to validate a docking results. I know ...
Some of the complexes (PDB ID: 1lpg, 1oyt, 1z9g, 1ryj, 3twp, 3utu, 5c2h) turned out to be impossible to prepare using the prepare_ligand4.py program with default settings. Most of the scoring functions (i.e., AutoDock 4.2, AutoDock Vina, AutoDock VinaXB, ∆Vina RF20, and...