AutoDock4/C2/Installation-of-AutoDock4-on-LInux-OS/English
Title of script: Installation of AutoDock4 on Linux OS
Author: Dr. Snehalatha Kaliappan and Sruthi Sudhakar
Keywords: AutoDock, Docking, autodock4, autogrid4, MGL Tools, ADT, PMV, Video tutorial.
Visual Cue | Narration |
Slide Number 1
Title Slide |
Welcome to this spoken tutorial on Installation of AutoDock4 on Linux OS. |
Slide Number 2
Learning Objectives |
In this tutorial, we will learn to,
Download AutoDock 4.2.6 installer files Install AutoDock 4.2.6 on Ubuntu Linux OS Install MGL Tools |
Slide Number 3
Learning Objectives |
Create aliases for using AutoDock Tools (ADT) and Python Molecular Viewer (PMV)
Open the GUI for ADT and PMV. |
Slide Number 4
System Requirement |
Here I am using,
AutoDock version 4.2.6 MGL Tools version 1.5.7 Google Chrome browser 96.0.4 Working internet connection |
Slide Number 5
Pre-requisites |
To follow this tutorial learner should be familiar with,
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Slide Number 6
Files to Download and website link AutoDock suite v4.2.6 MGL Tools v1.5.7 |
We need to download the following installer files from the official AutoDock website.
AutoDock suite version 4.2.6
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Opened https://autodock.scripps.edu/ in Firefox web browser.
Bring the cursor to the left side of the screen, Hover the mouse over Downloads link.
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I have opened the AutoDock website.
Hover the mouse over the Downloads link.
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https://autodock.scripps.edu/download-autodock4/
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The page refreshes.
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Highlight the AutoDock User Manual and Example links.
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Scroll down the page.
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Click on AutoDock v4.2.6 (Linux 64). | I am demonstrating the installation of AutoDock on Linux OS.
Hence I will click on the installer file for AutoDock Linux 64 bit. |
Go to Downloads folder and show autodocksuite-4.2.6-x86_64Linux2.tar | The compressed tar file, autodocksuite-4.2.6 downloads to the Downloads folder. |
Go back on the Downloads page.
Scroll down the page. To download the graphical user interface of AutoDock Tools (ADT) click here [1]click here Click on the link for MGL Tools.
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Back on the downloads page.
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https://ccsb.scripps.edu/mgltools/
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You will be directed to another page.
On this page information about MGL tools is given. |
Highlight the sentences on the page. | MGL tools comprises:
Python Molecular Viewer (PMV), a general purpose molecular viewer, and AutoDock Tools (ADT). It is a set of PMV commands specifically developed to support AutoDock users. |
Click on Downloads link seen on the left-side of the page. | Click on Downloads link seen on the left-side of the page. |
Scroll the page to see available installers. | The page refreshes.
It displays the latest stable version as 1.5.7. Here you will see installer files for various operating systems. |
Click on mgltools_x86_64Linux2_1.5.7.tar.gz | Click on Linux 64 tar ball installer file. |
Go to Downloads folder.
Show mgltools_x86_64Linux2_1.5.7.tar.gz |
The installer file automatically downloads to your Downloads folder. |
Show the files in the Downloads folder. | We have all the required installer files in the Downloads folder.
Now we have to install AutoDock and MGL tools. For this we will use the terminal. |
Press Ctrl, Alt and T keys simultaneously. | Open the terminal by pressing Ctrl, Alt and T keys simultaneously. |
Type,
cd Downloads, Press Enter. |
We have downloaded all the installers to the Downloads directory.
Let us change the directory to the Downloads folder.
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Cursor in the terminal. | Now let us extract and install the files one by one.
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Slide Number 7
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The required commands are provided in a text document in the Additional Materials section.
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Show the Desktop folder.
Double-click to open the gedit text file. |
I have saved the text file in a folder on the Desktop.
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From text file, copy the first command.
tar xvf autodocksuite-4.2.6-x86_64Linux2.tar Use Ctrl, Shift and V keys to paste the command on the terminal. Press Enter. |
In the document scroll down to the commands for extracting and installing the files.
Press Enter. |
Show x86_64Linux2 folder in the Downloads directory. | This will create a new directory x86_64Linux2 in the Downloads directory. |
Double-click on x86_64Linux2 to open it.
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I will double-click on the folder to open it.
autodock4 and autogrid4 in this folder.
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Cursor on the terminal.
Press Enter. |
We will move them to another directory where we keep the binaries.
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Cursor on the terminal.
cd x86_64Linux2 sudo mv autodock4 /usr/local/bin Paste it in the terminal at the prompt.
Press Enter.
sudo mv autogrid4 /usr/local/bin |
I will copy and paste this command to change the directory.
Give the system password when prompted. Copy the next command and paste it in the terminal.
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Type,
cd Downloads
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Come back to the Downloads directory to install the rest of the files.
Press Enter. |
Copy the command
tar xvzf mgltools_x86_64Linux2_1.5.7.tar.gz Paste it at the prompt and Press Enter. |
Back to the text document.
Copy the command to extract mgl tools.
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Show the folder mgltools_x86_64Linux2_1.5.7 in the Downloads directory. | This will create a folder in your Downloads directory as shown here. |
Type the commands,
Press Enter. |
Now to install it, we will go to the mgl tools directory.
./install.sh Press Enter. |
In the dialog box, the license agreement, click OK. | During installation, a dialog box with a message on Commercial usage pops up on the screen.
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Point to the message. | The terminal will show MGLTools installation complete. |
Cursor on the screen. | It will also ask to create aliases in order to run them. |
Cursor on the screen. | we will learn how to create aliases for MGL Tools, ADT and PMV |
Go to the Downloads folder and open mgltools_x86_64Linux2_1.5.7 folder. | Go to the Downloads directory and open mgltools folder. |
Double-click to open README file.
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Here you will see the README file.
Double-click to open the file.
Here you will see how to create aliases and add them to bashrc file.
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Type
cd ..
cd ..
clear
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Back to the terminal. Let us go back to the home folder.
type cd ..
type cd ..
I will now clear the screen.
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Cursor on bashrc file.
Scroll down to the end of the file. Type the following commands. alias adt='sudo /home/username/Downloads/mgltools_x86_64Linux2_1.5.7/bin/adt'
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This will open the bashrc file.
Scroll down to the end of the file.
As mentioned earlier, you may find the path in the README file. Change the path in the above command accordingly. I am changing the path that is appropriate for my system.
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Change the path to
home/snehalatha/Downloads/mgltools_x86_64Linux2_1.5.7/bin/adt'
Save the file. |
Change the path in the above command accordingly.
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In the terminal type the following command.
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Go back to the terminal and type the following command.
source ~/.bashrc
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Cursor on the screen.
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We have completed the step of creating aliases.
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Cursor on the ADT interface. | AutoDock Tools graphic interface opens as shown on the screen.
Close the ADT interface. Go back to the terminal and type pmv at the prompt. press Enter. PMV interface opens.
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Slide Number 8
Summary |
Let's summarize.
Downloaded AutoDock 4.2.6 installer files from the website. Installed them using a terminal on Ubuntu Linux 20.04 system. |
Slide Number 9
Summary |
Created aliases to use AutoDockTools (ADT) and Python Molecular Viewer (PMV).
Opened the GUI for ADT and PMV. |
Slide Number 10
Assignment |
As an assignment,
Use the link is given below.
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Slide Number 11
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Slide Number 12
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Slide Number 13
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Slide Number 14
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Slide Number 15
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Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India |
Thank you for joining. |