Congratulations! Now you are successfully create the config.txt file for AutoDock Vina input. PART: II ... Starts to analyzing the binding site. Performing Docking ...
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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.
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 config.txt file
Download executable 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:
cd - change directory
\ → 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 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.
![How to Use [PDF]](https://m.moam.info/img/260x300/how-to-use-pdf_647de705098a9e0a468b45fc.jpg)
