AutoDock Tutorial. 1. Prepare target protein for docking. AutoDock expects that the input protein has polar hydrogens and that all the water molecules have been . AutoDock, AutoGrid, AutoDockTools (GUI), and Open Babel Tutorial . C: Program Files (x86)MGLTools Introduction: How to obtain PDB. First docking method with flexible ligands. – AutoDock 3. Free energy force field and advanced search methods. AutoDockTools Graphical User Interface.

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