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AutoDock_Tutorial

The AutoDock Tutorial provides a step-by-step guide for preparing and executing molecular docking simulations using AutoDock tools. It outlines the necessary files, settings, and commands required to perform docking, including how to set up ligand and protein files, configure grid parameters, and execute docking runs. The tutorial is aimed at users familiar with molecular modeling and requires basic command line knowledge.

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tusharranjanmoharana
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9 views

AutoDock_Tutorial

The AutoDock Tutorial provides a step-by-step guide for preparing and executing molecular docking simulations using AutoDock tools. It outlines the necessary files, settings, and commands required to perform docking, including how to set up ligand and protein files, configure grid parameters, and execute docking runs. The tutorial is aimed at users familiar with molecular modeling and requires basic command line knowledge.

Uploaded by

tusharranjanmoharana
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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AutoDock Tutorial

Method · June 2020


DOI: 10.13140/RG.2.2.27339.21289

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Ammar Elmezayen
University of Texas Southwestern Medical Center
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All content following this page was uploaded by Ammar Elmezayen on 02 June 2020.

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Ammar Elmezayen
AUTODOCK TUTORIAL

• At the start of this tutorial, all you need is a directory (e.g., “Docking”) which consists of two files;
protein.pdb and ligand.mol2.
• 1. Open ADT tool of AutoDock.
• 2. File -> Preferences -> Set: change the startup directory.
• 3. Ligand -> Input -> Open: open your ligand mol2 file.
• 4. Ligand -> Torsion Tree -> Choose Torsions: decide on the rotatable bonds to be
considered.
• 5. Ligand -> Output -> Save as PDBQT: save your ligand file with “pdbqt” extension (e.g.
ligand.pdbqt). Type in the extension manually.
AUTODOCK TUTORIAL

• 6. Grid -> Macromolecule -> Open: Open your protein pdb file (e.g. protein.pdb), and
ADT tool will prompt a new window to save your protein into pdbqt file.
• 7. Grid -> Set Map Types -> Choose Ligand: select the ligand molecule from the list
shown.
• 8. Grid -> Grid Box: Select the number of grid points in x, y and z directions. Usually, the
default 40 is taken. However, you can increase or decrease that number in any direction.
From “Center” menu, select “Center on ligand”. Leave other parameters on default.
(Observe your grid box. Make sure that it covers the whole ligand as well as the binding
site).
AUTODOCK TUTORIAL

• File -> Close saving current: save your settings before closing. Otherwise, your settings will
be lost if the program is closed.
• 10. Grid -> Output -> Save GPF: save your gpf file (e.g. docking.gpf). Type in the extension
manually.
• 11. Check out the content of Grid Parameter File, docking.gpf (by Notepad).
• 12. Docking -> Macromolecule -> Set Rigid Filename: Select your macromolecule protein file
(e.g. protein.pdbqt).
• 13. Docking -> Ligand -> Choose: select your ligand. Leave everything on default and select
Accept.
AUTODOCK TUTORIAL

• 14. Docking -> Search Parameters -> Genetic Algorithm: set the number of GA Runs as
20.
• Also, set the maximum number of “evals” to long = 25000000 depending on the number
rotatable bonds. Leave other parameters on default and select Accept.
• 15. Docking -> Docking Parameters: Leave on default.
• 16. Docking -> Output -> Lamarckian GA: save your dpf file (e.g. docking.dpf). Type in
the extension manually.
• 17. Close your ADT tool.
AUTODOCK TUTORIAL

• In your working directory you should now have the following four files:
• ligand.pdbqt • receptor.pdbqt • docking.gpf • docking.dpf
• 18. Open “Windows PowerShell”: File -> Open Windows PowerShell -> Open Windows
PowerShell as administrator.
AUTODOCK TUTORIAL

• While you are inside your working directory, type the following Win/unix command:
Windows:
.\autogrid4.exe -p docking.gpf -l docking.glg
Unix:
autogrid4 -p docking.gpf -l docking.glg
• Once the program is completed, new files should appear in your working directory
including the map files.
AUTODOCK TUTORIAL

• These grid map files are necessary for the docking run. Now you are ready to dock. Type
the following:
Windows:
.\autodock4.exe -p docking.dpf -l docking.dlg
Unix:
autodock4 -p docking.dpf -l docking.dlg
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