The document provides instructions for downloading and installing AutoDock, AutoGrid, and AutoDockTools GUI. It then guides the user through preparing a receptor and ligand, setting up an AutoGrid calculation to generate maps, and running an AutoDock docking simulation to predict ligand-receptor binding conformations. The results table at the end lists the top 10 conformations ranked by binding energy.

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A Beginner’s Manual for AutoDock, AutoGrid, AutoDockTools (GUI), and
Open Babel: Video Tutorial Included
John P. Cahill
Drexel University
May 2015

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Video Tutorial Link: https://youtu.be/ZiuqSzqcD7M
Preface: Preliminary Knowledge
1. This instructional walkthrough will focus on the installation of AutoDock and AutoGrid
on a Microsoft-based operating system
a. There are essentially no “minimum requirements” to install or run AutoDock,
AutoGrid, and AutoDockTools GUI
i. However, insufficient RAM appears to be the only reasonable hardware
limitation. My personal data logging shows that the calculations directly
preformed in this guide require roughly 650MBs of RAM at maximum.
ii. However, this number only takes into account the following
processes/threads: Python, AutoDock, AutoGrid, and AutoGridTools. It
does not take into account background processes or OS requirements.
iii. Thus, more complex computations, more receptors, more ligands, etc will
require more system resources
iv. Host computer hardware specifications:
1. Processor: Intel i7 4790K @ 4.0GHz – Quad Core
a. Note: Major influence. Clock speed will greatly influence
the speed at which computations can be performed.
However, any practical Intel or AMD processor can run the
AutoDock suite.
2. RAM: Corsair Vengeance Pro 32GB
a. Recommendation: Minimum of 4GB of system-wide RAM;
if possible 8GB of system-wide RAM for optimal
performance.
i. 32-bit Operating Systems are limited to 4GB of
RAM
ii. 64-bit Operating Systems can utilize ~192GB
3. Graphics Card: NVIDIA GTX 970
a. NOTE: Negligible. A graphics card cannot be used to speed
up computations since the AutoDock suite relies solely on
CPU threads for calculations.
4. Hard Drive: Samsung 850 Pro SSD
a. Note: Negligible. System logs did not show high disk
utilization. 4200-5400RPM drives may approach their
maximum read/write throughput but a 7200RPM or solid-
state drive is sufficient.
5. Operating System: Windows 8.1 Pro 64-bit

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b. I recommend installing a widget that allows you to visually monitor CPU and
Memory utilization. Unusually low CPU utilization during a computation can be
an indicator of an incorrectly entered command.
Introduction: How to Download and Install the AutoDock Suite
1. This step will walk the user through the download and installation process for the
AutoDock suite and GUI interface
a. The AutoDock Suite can be downloaded from: http://autodock.scripps.edu/
under the “Downloads” navigational tab
i. NOTE: This suite contains AutoDock and AutoGrid
b. Download AutoDock Suite Windows Executable Installer
i. At the time of writing, http://autodock.scripps.edu/ is offline. This guide
will be updated to include an install tutorial.
c. Download AutoDockTools (ADT) Windows Executable Installer
i. At the time of writing, http://autodock.scripps.edu/ is offline. This guide
will be updated to include an install tutorial.
2. Ensure program initializes correctly
a. The most common error seems to be Python responding with an “Error 2”
message. This means that the location of a file cannot be found or opened.
Likely, you have not selected the proper location for the file.
b. Furthermore, this is most common when running the AutoDock or AutoGrid
command from GUI. Even though the program pathway is filled in, it may be
necessary to manually locate the respective program in:
i. AutoDock and AutoGrid:
1. C:Program Files (x86)The Scripps Research
InstituteAutodock4.2.6.
ii. AutoDockTools GUI (also includes AutoDock and AutoGrid)
1. C:Program Files (x86)MGLTools-1.5.6
Introduction: How to obtain PDB files
1. Using a web browser navigate to: http://www.rcsb.org/pdb/home/home.do
2. Search a PDB ID, macromolecule, ligand, author, or other identifying attribute
a. In this tutorial I will use the following PDB IDs:
i. Receptor: 2ZCK
ii. Ligand: ZAP
3. Selecting the 2ZCK should yield a result titled “Crystal structure of a ternary complex
between PSA, a substrat-acyl intermediate and an activating antibody”
a. The “Molecular Description” tab will detail all the subcomponents of the PDB file
we are about to download. In this case, it contains the Prostate-specific antigen,
KGISSQY, monoclonal antibody 8G8F5 Fab

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b. The PGA we are interested in is denoted as chain P in the file. Take note of this
as we will have to separate this chain from the others.
4. To the right of the bolded PDB ID name there are three options: Display Files, Download
Files, and Download Citation.
a. Display Files will allow you to view, usually in HTML or plain-text, the contents of
the PDB file
b. Download Files will allow you to download the file in several different formats.
c. Download Citations will allow you to import this article into a reference manager
such as EndNote.
5. Select the Download Files tab and click “PDB File” text. A file called “2ZCK.pdb” should
be downloaded to your web browser’s default download folder.
a. If your web browser does not download the .pdb file correctly or shows you the
viewable file instead, check your browser settings or right click the “PDB File
(text)” and use the “save link as…” function to manually download it.
6. Using the same procedure, search PDB ID: ZAP
7. In some cases, such as this one, a PDB file cannot be downloaded
8. Under the ligand’s download files tab the only formats available are Structure Data File
and mmCIF component definition
a. Select the Structure Data File
9. This will download a .SDF file to your web browser’s download folder
a. Similarly, in some cases it will be necessary to use the “save link as…” function.
My current setup requires me to use this function by going to Display Files
instead of Download Files and right clicking the SDF option.
10. Please ensure that you have successfully downloaded the “ZAP_ideal.sdf” file at this
point.
Runtime Environment: Open Babel
1. Using your web browser, navigate to:
http://openbabel.org/docs/dev/Installation/install.html
2. Run the installer with all default options
3. The setup does not offer to create a desktop shortcut by default
4. Create one by navigating to: C:Program Files (x86)OpenBabel-2.3.2
a. Note: The actual program is called “obgui”
5. Run the Open Babel program
6. For this tutorial, we must convert the ligand from a SDF file to a PDBQT file in order to
use it with AutoDock
a. Select the SDF format on the input format side and select PDBQT on the output
side
b. Input the pathname for the SDF file

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c. Choose a pathname for the outputted PDBQT file
i. WARNING: At this point, you should be saving all files to the
ADTworkspace folder on the drive’s root
7. Click the CONVERT button and wait for it to complete the conversion process
Runtime Environment: AutoDockTools (GUI)
1. Click the AutoDockTools desktop shortcut to initialize the program.
a. Two terminal windows should open. Do not attempt to exit these when using
AutoDockTools. Closing either terminal window will force quit the
AutoDockTools GUI application.
b. AutoDockTools relies on the AutoDock and AutoGrid programs to function
correctly. These two command line programs are located in: C:Program Files
(x86)The Scripps Research InstituteAutodock4.2.6
2. AutoDockTools, on Windows 7 and higher, has issues dealing with filenames that
contain spaces. This is likely fixable by updating a dependency but I have not found a
resolution yet.
a. Thus, it is easiest to use directories that are at the hard drive’s root without any
spaces.
b. A shortcut can then be created for the desktop, if desired.
3. Within AutoDockTool’s GUI select: File>Preferences>Set
a. Change the Startup Directory to a folder at the Hard Drive’s Root
b. This folder will contain all PDB and related files.
i. WARNING: In my experience, failing to do this can cause issues with
AutoDock and AutoGrid when attempting to preform calculations.
Typically they will error out with “cannot open or locate file” response
and will create blank output files.
ii. Example: C:ADTworkspace
c. Click “Make Default” and “Set” to ensure that these settings survive program
resets
4. Place the 2ZCK.pdb file into the ADTworkspace folder
5. At this point, you are now ready to begin loading molecules into the interface.
Runtime Environment: Reading a receptor and ligand in AutoDockTools
1. Click File>Read Molecule
a. Load the 2ZCK PPDB file (receptor). Do not load the ligand here.
2. Click the down arrow next to the molecule that was just read. In this case, you should
see a P, S, L, and H chain.
3. Select the selection box next to the S, L, and H chain. This should highlight a majority of
the 2ZCK molecule we just loaded with yellow selection marks.

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4. Click Edit>Delete>Delete Selected Atoms and then click Continue.
a. At this point, you have successfully isolated the PSA from the other chains.
5. To prepare the PSA as a receptor for autodock and autogrid there are a few preliminary
steps that must be done:
a. Edit>Delete Water
b. Edit>Hydrogens>Add Hydrogens
i. Use default settings: All Hydrogens, noBondOrder, yes
ii. Click OK
c. Edit>Hydrogens>Merge Non-Polar
d. Edit>Charges>Compute Gasteiger Charge
6. At this point, you have successfully prepared the receptor for AutoDock and AutoGrid
calculations
a. You can save this molecule by going to File>Save>Write PDB
b. This will allow you to reset the program and bypass these steps, if needed
c. Make sure that you do not get this molecule confused with the original
d. NOTE: At this point, you cannot save it as a PDBQT file as it does not have the
proper attributes yet
7. Load in the Ligand File
a. Click Ligand>Input>Open and select ZAP.pdbqt
b. Click Ligand>Torsion Tree>Detect Root
8. At this point, we have successfully loaded both a receptor and ligand. We are now
prepared to setup AutoGrid calculations.
9. Click the Grid Tab
a. Grid>Macromolecule>Choose
i. It will prompt you to save this file as a PDBQT. Ensure that you save it as
filename.pdbqt
b. Grid>Select Map Types>Choose Ligand
i. Select ZAP
c. Grid>Select Map Types>Set Up Covalent Map
i. Click the downarrow next to 2ZCK_P to reveal all the residues. Locate
SER195 and click the down arrow next to it. Click the select box for
SER195’s OG atom. Then click the checkbox for “Use selection for
Attachment Atom”
ii. It will prefill the coordinates.
iii. Change the “Energy Barrier Height” to 1000
iv. Change the “Half-width (angstrom)” to 5.00
v. Click Accept
d. Grid>Grid Box
i. Set “number of points in x-dimension” to: 100
ii. Set “number of points in x-dimension” to: 100
iii. Set “number of points in x-dimension” to: 100

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iv. Set “Spacing (angstrom)” to: 0.200
v. Set “Center Grid Box” to:
1. X center: -36.636
2. Y center: -37.475
3. Z center: -21.304
vi. NOTE: it is often easiest to right click the dial and manually input the
values using keypad entry
vii. CAUTION: You MUST click File>Close Saving Current
1. If you do not, all inputted data will be discarded
viii. Deselect the OG atom from SER195 from the Dashboard
e. Grid>Output>Save GPF
i. CAUTION: You must put this in the main directory we designated earlier
(the one that all the PDBs and PDBQTs have been saved in)
ii. CAUSTION: You must also manually amend the .gpf extension
iii. Click SAVE
10. At this point we have setup the AutoGrid parameters but we have not issued the
AutoGrid “run” command
a. Click Run>AutoGrid
b. Do the following:
i. Program Pathname: click browse and navigate to the autogrid4
application. It should be located in: C:Program Files (x86)The Scripps
Research InstituteAutodock4.2.6
ii. Parameter Filename: locate your grid.gpf file you saved in the program’s
workspace
iii. Log Filename: This should be automatically filled after selecting the
Parameter Filename. If it is not create a grid.glg file in the workspace
directory.
iv. Click Launch
1. NOTE: this is where a CPU utilization monitor is handy. You should
see an increased load. On my system core 4 and 3 are heavily
utilized (approximately 50-90%).
2. NOTE: If the process manager does not remain open for at least a
few seconds, you have incorrectly configured the program or the
settings and DO NOT have a viable output file
a. In my experience, this process takes about 40-60 seconds
c. AutoGrid will close the Process Manager window when it is completed. When
this happens go to Grid>Edit GPF
i. Click Read and open the grid.gpf file we just created to confirm it is valid.
You should see more values populate after reading the file. Click Cancel
to exit.

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11. At this point, we have ran AutoGrid and created the necessary maps required for
AutoDock to run.
a. Click Docking>Macromolecule>Select Rigid Filename and select 2ZCK.pdbqt
b. Click Docking>Ligand>Choose and select ZAP
i. Use defaults. Click Accept.
c. Click Docking>Search Parameters>Genetic Algorithm
i. Change “Number of GA Runs” to 25
ii. Confirm “maximum number of evals” is set to MEDIUM
iii. Click accept.
d. Click Docking>Output>Lamarckian GA (4.2)
i. Save output as dock.dpf
e. Click Run>AutoDock
i. Program Pathname: Browse for AutoDock4 application which should be
located in: C:Program Files (x86)The Scripps Research
InstituteAutodock4.2.6
ii. Parameter Filename: locate the dock.dpf file we just saved in the
workspace
iii. Log Filename: this field should automatically populate
iv. Click LAUNCH
1. NOTE: If the process manager does not remain open for at least a
few seconds, you have incorrectly configured the program or the
settings and DO NOT have a viable output file
2. This process took: 28 minutes and 26 seconds
12. Once AutoDock completes the calculations, you can then go to:
Analyze>Confirmations>Play, ranked by energy
a. This will show all binding confirmations in order of energy
13. At this point, you may analyze the results, interactions, and confirmations as needed

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Results
Ligand
Binding
Energy
Intermol
Energy
Internal
Energy
Torsional
Energy
Unbound
Energy
dock -6.16 -9.14 -2.08 2.98 -2.08
dock -6.51 -9.49 -1.3 2.98 -1.3
dock -5.78 -8.77 -1.47 2.98 -1.47
dock -6.06 -9.04 -2.03 2.98 -2.03
dock -7.07 -10.06 -0.99 2.98 -0.99
dock -8.04 -11.02 -1.21 2.98 -1.21
dock -6.19 -9.17 -2.11 2.98 -2.11
dock -6.93 -9.91 -2.04 2.98 -2.04
dock -7.06 -10.05 -1.7 2.98 -1.7
dock -7.11 -10.1 -1.62 2.98 -1.62
dock -7.28 -10.26 -1.63 2.98 -1.63
dock -7.73 -10.72 -1.53 2.98 -1.53
dock -8.12 -11.1 -1.43 2.98 -1.43
dock -7.63 -10.61 -1.17 2.98 -1.17
dock -7.08 -10.06 -1.76 2.98 -1.76
dock -7.62 -10.6 -1.32 2.98 -1.32
dock -8.94 -11.93 -1.06 2.98 -1.06
dock -6.09 -9.08 -1.98 2.98 -1.98
dock -8.42 -11.4 -1 2.98 -1
dock -6.83 -9.81 -1.66 2.98 -1.66
dock -7.61 -10.6 -1.28 2.98 -1.28
dock -7.64 -10.62 -1.16 2.98 -1.16
dock -7.91 -10.89 -1.28 2.98 -1.28
dock -7.49 -10.48 -1.21 2.98 -1.21
dock -7.49 -10.47 -1.5 2.98 -1.5
Table 1: This table contains the resultants of the AutoDock calculation preformed above. The
receptor is a prostate-specific antigen and the ligand is [N-(BENZYLOXYCARBONYL)AMINO](4-
AMIDINOPHENYL)METHANE-PHOSPHONATE (PDB ID: ZAP).

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Figure 1: PSA obtained from 2ZCK (PDB ID) bound with highest ranked ligand confirmation.
Ligand was obtained from ZAP (PDB Ligand ID). This figure depicts the highest ranked
confirmation from table 1.