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This May Consist of 2 Major Parts: How To Use Autodock Vina?

This document provides instructions for using AutoDock Vina to perform molecular docking simulations. It describes: 1) How to prepare the config.txt input file by specifying the receptor and ligand PDBQT files and grid size. 2) How to run AutoDock Vina by placing the config.txt file and executable in a folder, setting the path, and running vina with the "--config" flag. 3) Vina will then score and analyze the binding site, perform docking, and print the results including the final binding energy.

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76 views7 pages

This May Consist of 2 Major Parts: How To Use Autodock Vina?

This document provides instructions for using AutoDock Vina to perform molecular docking simulations. It describes: 1) How to prepare the config.txt input file by specifying the receptor and ligand PDBQT files and grid size. 2) How to run AutoDock Vina by placing the config.txt file and executable in a folder, setting the path, and running vina with the "--config" flag. 3) Vina will then score and analyze the binding site, perform docking, and print the results including the final binding energy.

Uploaded by

thamizh555
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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HOW TO USE AUTODOCK VINA?

This may consist of 2 major parts

PART: I Prepare the config.txt file

PART: II Perform the AutoDock Vina

PART: I

How to prepare the ‘config.txt’ file for AutoDock Vina job?


STEP: 1

Edit the .pdbqt file names and grid size in config.txt file

.pdbqt files name of the receptor


and ligand, respectively

No of conformers (like AutoDock GA run)

I don’t have idea about this statement,


kindly, keep this as it is
Strictly, follow this, space and lower case may sensitive

If you performed docking already using AutoDock, you could able to get these grid
values from your ‘protein.gpf’ file.

If you wish to create or edit this ‘config.txt’ file in Windows environment you
better to use Notepad++ or ConTEXT or TextPad editor(s)

Congratulations! Now you are successfully create the config.txt file for AutoDock Vina input

PART: II
Now, We’re going to perform the AutoDock Vina
Log in to linux (Ubuntu)
STEP: 1 Create a folder

SETP:2 Keep the following files in the mother folder

We just before created Download executable


config.txt file vina (linux) file

Already prepared .pdbqt files


while performing AutoDock

(i) protein.pdbqt

(ii) ligand.pdbqt (You could able to prepare these files from AutoDock Tools)

(iii) vina program file (You could able to download this file from web)

(iv) Just before we’re created the config.txt file for our ligand and their target
receptor (Model file has been enclosed)
STEP: 3 Open the Terminal

Statement: 1 Set the PATH of the mother folder

Statement explanation:

\ → This backward slash an indicates the space section.


I have type the Vina(space)Docking. So, I given the
statement Vina\(space) Docking CAPITAL letters are
cd - change directory
case sensitive
Statement: 2

vina comment (Important)

Statement explanation:

Statement File name

Statements:
cd /home/mani/Desktop/Vina\ Docking/
./vina --config config.txt

Start scoring function


Starts to analyzing the binding site

Performing Docking
Print the results

Final binding energy

AutoDock Vina Successful Completed

for give the opportunity to teach you

For more details visit: http://vina.scripps.edu/manual.html

Cite: O. Trott, A. J. Olson,"AutoDock Vina: improving the speed and accuracy of


docking with a new scoring function, efficient optimization and multithreading”,
Journal of Computational Chemistry 31 (2010) 455-461.

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