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Go to Ligand > Input > Open to ensure the ligand preparation module is active.

Hydrogens are essential for accurate force-field calculations and must be added to all polar and non-polar atoms.

Go to and load your small molecule .pdb or .mol2 file.

Official repository – The Scripps Research Institute (via CCSB). download autodock tools work

Do you need help finding to test your setup?

Go to to define active rotatable bonds.

However, for full control over docking parameters, flexible residues, and detailed analysis, Go to Ligand > Input > Open to

Comprehensive Guide: How to Download and Set Up AutoDock Tools for Molecular Docking

The primary source for downloading AutoDock Tools is the at Scripps Research. Version: The latest stable version is typically 1.5.7 .

Are you planning to use or the newer AutoDock Vina ? Official repository – The Scripps Research Institute (via

Apply Gasteiger , Kollman , or AutoDock4 charges to your molecules to simulate electrostatic interactions.

AutoDock and MGLTools are designed to run on older systems and do not have high computational demands. The software will work on almost any computer capable of running a modern Windows, Linux, or macOS operating system. The primary requirement is administrative permissions to install the software.

, which serves as the graphical interface for setting up molecular docking simulations. 1. Downloading the Software The most reliable way to get The Scripps Research Institute 's official tools is through the MGLTools downloads page Official Source: MGLTools Download Page Version Selection:

Drag and drop the MGLTools application folder into your directory.