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AutoDock Tutorial v1.2

This document provides instructions for using various molecular docking software programs including AutoDock, AutoDock VINA, AutoDockTools (ADT), PyRx, and PyMol. It outlines the necessary downloads, installation process, steps for preparing the macromolecule and ligands, and running docking simulations with AutoDock VINA in PyRx. The macromolecule preparation involves removing waters, existing ligands, and additional subunits before adding polar hydrogens. Ligand preparation may involve energy minimization and generating PDBQT files using either PyRx or ADT depending on the ligand. Docking is then run using the VINA wizard in PyRx.

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Judith Nelson
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131 views

AutoDock Tutorial v1.2

This document provides instructions for using various molecular docking software programs including AutoDock, AutoDock VINA, AutoDockTools (ADT), PyRx, and PyMol. It outlines the necessary downloads, installation process, steps for preparing the macromolecule and ligands, and running docking simulations with AutoDock VINA in PyRx. The macromolecule preparation involves removing waters, existing ligands, and additional subunits before adding polar hydrogens. Ligand preparation may involve energy minimization and generating PDBQT files using either PyRx or ADT depending on the ligand. Docking is then run using the VINA wizard in PyRx.

Uploaded by

Judith Nelson
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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AutoDock Tutorial (v1.

1)
I) Needed Downloads:
AutoDock 4.2 (registration required)
AutoDockVINA

Note: These websites have


tutorials and information
that will be useful to learn

AutoDockTools (ADT)
PyRx
PyMol (registration required)

II) Installation
1. Once youve downloaded the programs, install them in their recommended
folders. Take note of where autodock4.exe, autogrid4.exe, and vina.exe are
installed.
2. In PyRx, Go to Edit Preferences
a. Browse to the locations of the .exe files listed in step II-1

III) Macromolecule Preparation


The first thing that you need to do is prepare your macromolecule for docking. There
are simple ways to do this, but there are a host of subtle changes and steps you can
take if problems arise.
1. Simple Macromolecule Prep
a. Download PDB file from Protein Data Bank
b. Open PDB in PyMol or AutoDockTools (ADT)
i. Remove waters
1. in PyMol, simply select them all at once after clicking on
the S icon for sequence (to see them in the PDB
sequence), then delete selected.
2. in ADT, go to Select Select from String. In the box for
Residue type HOH*, then click Add. Then go to Edit
Delete Delete Atom Set

ii. Remove ligand(s) from the active site


1. Same as waters in PyMol
2. In ADT,
a. click on Float Dashboard Widget

b. Then tab down to see the residues; find your ligand,


select it, and delete it similar to removing waters.

iii. If your protein has repeat subunits, you may want to remove
them also
iv. Add Polar hydrogens
1. Go to Edit Hydrogens Add
2. Select Polar Only, leave the rest the same, click OK
c. Save new PDB
i. Whether in PyMol of ADT, save as a PDB (not a PDBQT),
preferably in the same location where you keep all
Macromolecule PDBs, with a slightly different name than the
original PDB.
d. Open PyRx
Note: This creates a
PDBQT in the
PyRx\Macromolecules
folder, which you can see
in the Navigator window
under the AutoDock tab.

i. Click on the Load Molecule Icon, browse and select your PDB.
ii. Once the PDB is in the Navigator screen, right click it, select
Autodock Make Macromolecule

2. More detailed instructions can be found here

III) Ligand Preparation


1. Start with a stereochemically accurate chemdraw structure.
2. Open ChemBio3D
a. Copy and paste your chemdraw picture
b. Minimize the energy (Calculation MM2 Minimize Energy)
c. Save as a PDB
3. Make PDBQT in PyRx directly, or for ligands containing aromatic nitrogens (ie
triazoles), you will need to use ADT.
a. PyRx
Note: This creates a
PDBQT in the
PyRx\Ligands folder

i. Open the PDB in the PyRx


ii. Right click on the ligand name in the Navigator window, select
Autodock Make Ligand
b. ADT (for compounds incorrectly protonated at heteroatoms)
i. Open PDB in ADT by clicking Ligand Input Open
ii. Save PDBQT by clicking Ligand Output Save as PDBQT
1. Save it in the PyRx Ligand folder (for instance,
C:\Users\Berkley\.mgltools\PyRx\Ligands). If you have
PyRx open, right click on the Ligands folder in the
Navigator window, and choose Refresh. Your ligand will
now show up with as a correctly protonated PDBQT.

IV) Running Vina in PyRx


This is extremely simple and intuitive. Click on the Vina wizard at the bottom window
in PyRx and follow the instructions. Multiple ligands may be chosen at once. Grid
size must encompass the active site, but may be much larger. Vina is fast enough
that large grid sizes are not a burden.

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