This document provides instructions for performing molecular docking simulations using Autodock 4. It discusses downloading and installing Autodock, preparing receptor and ligand files in pdbqt format, setting up a grid parameter file to define the docking grid, preparing an Autodock parameter file to define the docking parameters, running Autodock to perform the docking simulation, and analyzing the results to view and evaluate the predicted binding modes.

1. Email: shah.sapan@rediffmail.com
Molecular Docking using
Autodock 4
Sapan K. Shah
Asst. Prof.
Priyadarshini J. L. College
of Pharmacy, Nagpur

2. Email: shah.sapan@rediffmail.com
What is Docking?
Molecular docking is a study of
how two or more molecular
structures, eg. drug and receptor,
match along to be a perfect fit
(Gane & Dean, 2000).
“Predicting the best ways two
molecules will interact.
• Obtain the 3D structures of
the two molecules.
• Locate the best binding site.
• Determine the best binding
modes

3. Email: shah.sapan@rediffmail.com

4. Email: shah.sapan@rediffmail.com
1. Download and Installation of AutoDock
3. How to prepare a ligand file for AutoDock 4
2. How to prepare a receptor file for AutoDock4
4. How to prepare a grid parameter file for AutoGrid 4
5. How to prepare a docking parameter file for AutoDock4
6. How To Run AutoDock?
7. How To Analyse AutoDock Results
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5. Email: shah.sapan@rediffmail.com
• AutoDock is a suite of automated docking
tools. It is designed to predict how small
molecules, bind to a receptor of known 3D
structure.
• Two generations of software: AutoDock 4
and AutoDock Vina
Download and Installation of AutoDock
Step 1
Download a new executable from:
http://autodock.scripps.edu/downloads

6. Email: shah.sapan@rediffmail.com
How to prepare a receptor file for AutoDock4Step 2
1. Download Protein Data Bank
https://www.rcsb.org/
2. Fetch Protein data file
directly
File / Open…target.pdb
Delete water molecules
 GO TO AUTODOCK
Add Hydrogen/Add Polar Only
Remove unwanted residue
Add Charges-
1) Kollman charge
2) Compute Gasteiger charges
Assign hydrogen-AD4 type only
Save as ….target.pdbqt

7. Email: shah.sapan@rediffmail.com
How to prepare a ligand file for AutoDock 4
Draw and save as mol2 or pdb file
1. Zinc database:
http://zinc12.docking.org/
2. Drug bank:
https://www.drugbank.ca/
3. PubChem:
https://pubchem.ncbi.nlm.nih.gov/#query=aspirin
4. Chemspider
http://www.chemspider.com/
5. ChemDB
http://cdb.ics.uci.edu/
6. ChemMBL
https://www.ebi.ac.uk/chembl/
7. Using Avogadro- My favorite
 LIGAND /
INPUT /
OPEN
 SAVE AS..
ligand.pdbqt
 LIGAND /
OUTPUT
 GO TO
AUTODOCK
Step 3

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*Source: NPTEL/CADD

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How to prepare a grid parameter file for AutoGrid 4
Step 4
Grid map optimization
Select Grid / Macromolecule / Choose..target……Save as
target.pdbqt
Select Grid /Grid box…… Grid Parameters….File / close
saving current
Grid /Output / Save target.gpf …… target.gpf

10. Email: shah.sapan@rediffmail.com
How to prepare a docking parameter file for AutoDock4
Docking /Macromolecule /
Set rigid filename
Docking /Ligand / Choose…ligand
Docking /Search parameters /
Genetic algorithm. Accept Docking /Docking
parameters…accept
Docking /Output / Lamarckian…. Save
target.dpf
Step 5

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How To Run AutoDock?Step 6
Run Autogrid
•Select tab RUN>>RUN AUTOGRID>>Click BROWSE>>Select AUTOGRID APPLICATION FILE in PROGRAM PATH
NAME>>Click BROWSE>>Select TARGET.GPF in PARAMET FILE NAME>>Click LAUNCH
Run Autodock
•Select tab RUN>>RUN AUTODOCK>>Click BROWSE>>Select AUTODOCK APPLICATION FILE in PROGRAM PATH
NAME>>Click BROWSE>>Select TARGET.DPF in PARAMET FILE NAME>>Click LAUNCH
Run Autodock Vina
• OPEN COMMAND PROMPT
• Type “C: foldername“ for selecting path
• Type "C:Program Files (x86)The Scripps Research InstituteVinaVina.exe" --
receptor target.pdbqt --ligand ligand.pdbqt --config conf.txt --log log.txt --out
output.pdbqtxt]

12. Email: shah.sapan@rediffmail.com
How To Analyse AutoDock ResultsStep 7
Analyse / Docking
/ Open/target.dlg
Analyse /
Macromolecule /
Choose/target
Analyse /
Conformations /
Play….

show
conformations
Analyse /
openautodockvina
results/
Open/outputfile

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