Difference between revisions of "AutoDock4/C2/Installation-of-AutoDock4-on-LInux-OS/English"

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(Created page with " '''Title of script''': '''Installation of AutoDock4 on Linux OS''' '''Author:''' Dr. Snehalatha Kaliappan and Sruthi Sudhakar Keywords: AutoDock, Docking, autodock4, autog...")
 
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Keywords: AutoDock, Docking, autodock4, autogrid4, MGL Tools, ADT, PMV, Video tutorial.
+
'''Keywords''': AutoDock, Docking, autodock4, autogrid4, MGL Tools, ADT, PMV, Video tutorial.
  
  
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'''Title Slide'''
 
'''Title Slide'''
−
|| Welcome to this tutorial on Installation of '''AutoDock4''' on '''Linux OS'''.
+
|| Welcome to this spoken tutorial on Installation of '''AutoDock4''' on '''Linux OS'''.
 
|-
 
|-
 
|| '''Slide Number 2'''
 
|| '''Slide Number 2'''
Line 80: Line 80:
 
https://autodock.scripps.edu/
 
https://autodock.scripps.edu/
  
−
|| We need to download the following installer files from the official '''AutoDock '''website.
+
|| We need to download the following installer files from the official '''AutoDock ''' website.
  
 
AutoDock suite version 4.2.6
 
AutoDock suite version 4.2.6
Line 109: Line 109:
  
  
−
Click on '''AutoDock4''' option.  
+
Click on the '''AutoDock4''' option.  
 
|-
 
|-
 
|| [https://autodock.scripps.edu/download-autodock4/ https://autodock.scripps.edu/download-autodock4/]
 
|| [https://autodock.scripps.edu/download-autodock4/ https://autodock.scripps.edu/download-autodock4/]
Line 118: Line 118:
  
  
−
On this page you can see downloadable installer files for '''Linux''', '''Mac '''and '''Windows OS.'''
+
On this page you can see downloadable installer files for '''Linux''', '''Mac ''' and '''Windows OS'''.
  
 
|-
 
|-
Line 137: Line 137:
  
  
−
Similarly save the '''Examples''' file.
+
Similarly, save the '''Examples''' file.
  
  
−
The files will be downloaded to your download folder
+
The files will be downloaded to your '''Downloads''' folder.
  
 
|-
 
|-
Line 161: Line 161:
  
  
−
We need to also download the '''MGL''' tools which include''' ADT.'''
+
We need to also download the '''MGL''' tools which include ''' ADT'''.
  
  
Line 170: Line 170:
  
  
−
'''To download the graphical user interface AutoDock Tools (ADT) click[https://ccsb.scripps.edu/mgltools/  ][https://ccsb.scripps.edu/mgltools/ here].'''
+
'''To download the graphical user interface of AutoDock Tools (ADT) click here[https://ccsb.scripps.edu/mgltools/  ][https://ccsb.scripps.edu/mgltools/ here].'''
  
  
Line 179: Line 179:
  
 
Scroll the page
 
Scroll the page
−
|| You will be redirected to another page.
+
|| You will be directed to another page.
  
 
On this page information about '''MGL''' tools is given.
 
On this page information about '''MGL''' tools is given.
Line 195: Line 195:
 
|-
 
|-
 
||Click on '''Downloads '''link seen on the left-side of the page.
 
||Click on '''Downloads '''link seen on the left-side of the page.
−
|| 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.
 
||Scroll the page to see available installers.
Line 202: Line 202:
 
It displays the latest stable version as 1.5.7.
 
It displays the latest stable version as 1.5.7.
  
−
Here you will see installer files for various '''OS'''.
+
Here you will see installer files for various '''operating systems'''.
 
|-
 
|-
 
||Click on '''mgltools_x86_64Linux2_1.5.7.tar.gz'''
 
||Click on '''mgltools_x86_64Linux2_1.5.7.tar.gz'''
Line 220: Line 220:
 
|-
 
|-
 
||Press Ctrl, Alt and T keys simultaneously.
 
||Press Ctrl, Alt and T keys simultaneously.
−
|| Open the terminal by pressing '''Ctrl''', '''Alt '''and '''T''' keys simultaneously.
+
|| Open the terminal by pressing '''Ctrl''', '''Alt ''' and '''T''' keys simultaneously.
  
 
|-
 
|-
Line 241: Line 241:
 
Press''' Enter.'''
 
Press''' Enter.'''
 
|-
 
|-
−
||
+
||Cursor in the terminal.
 
||| Now let us extract and install the files one by one.
 
||| Now let us extract and install the files one by one.
  
Line 264: Line 264:
  
 
Double-click to open the '''gedit text''' file.
 
Double-click to open the '''gedit text''' file.
−
|| I have saved the text file in a folder on the desktop.
+
|| I have saved the text file in a folder on the '''Desktop'''.
  
  
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−
Copy the command as shown, by pressing '''Ctrl''' and''' C''' keys together.
+
Copy the command as shown, by pressing '''Ctrl''' and ''' C''' keys together.
  
  
Line 285: Line 285:
  
  
−
Use '''Ctrl,''' Shift and '''V''' keys to paste the command on the terminal.
+
Use '''Ctrl,''' '''Shift''' and '''V''' keys to paste the command on the terminal.
  
 
Press '''Enter'''.
 
Press '''Enter'''.
Line 332: Line 332:
  
  
−
Press '''Enter '''to execute the command.
+
Press '''Enter ''' to execute the commands.
 
|-
 
|-
 
|| Cursor on the terminal.
 
|| Cursor on the terminal.
Line 339: Line 339:
 
Copy the command by pressing Ctrl and C keys together.
 
Copy the command by pressing Ctrl and C keys together.
  
 +
cd x86_64Linux2
 +
 +
sudo mv autodock4 /usr/local/bin
  
 
Paste it in the terminal at the prompt.  
 
Paste it in the terminal at the prompt.  
Line 349: Line 352:
  
 
Press Enter. Give the system password when prompted.
 
Press Enter. Give the system password when prompted.
−
|| I will copy and paste this command to change the directory:
 
  
 +
sudo mv autogrid4 /usr/local/bin
  
−
cd x86_64Linux2
+
|| I will copy and paste this command to change the directory.
  
  
 
Copy the next command to move the files to user local bin.
 
Copy the next command to move the files to user local bin.
  
−
sudo mv autodock4 /usr/local/bin
 
  
−
Press '''Enter'''. Give the system password when prompted.
+
Press '''Enter'''.  
  
−
Copy the next command and paste it in the terminal.
+
Give the system password when prompted.
−
 
+
−
sudo mv autogrid4 /usr/local/bin
+
  
 +
Copy the next command and paste it in the terminal.
  
  
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−
Press Enter
+
Press '''Enter'''.
−
|| Come back to the downloads directory to install the rest of the files.
+
|| Come back to the '''Downloads''' directory to install the rest of the files.
  
  
−
Type,  
+
Type, cd and Press '''Enter'''.
−
 
+
−
cd
+
−
 
+
−
 
+
−
Type,
+
  
  
−
Cd Downloads
+
Type,  cd space Downloads Press '''Enter'''.
 
|-
 
|-
 
|| Copy the command  
 
|| Copy the command  
Line 400: Line 396:
 
|| Back to the text document.
 
|| Back to the text document.
  
−
Copy the command to extract '''mgl '''tools.  
+
Copy the command to extract '''mgl ''' tools.  
  
  
Line 409: Line 405:
 
|-
 
|-
 
||Show the folder '''mgltools_x86_64Linux2_1.5.7 '''in the Downloads directory.
 
||Show the folder '''mgltools_x86_64Linux2_1.5.7 '''in the Downloads directory.
−
|| This will create a folder in your '''Downloads''' folder as shown here.
+
|| This will create a folder in your '''Downloads''' directory as shown here.
  
 
|-
 
|-
Line 437: Line 433:
 
|-
 
|-
 
||In the dialog box, the license agreement, click '''OK'''.
 
||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,
+
|| During installation, a dialog box with a message on Commercial usage pops up on the screen.
  
  
−
Read the message and click''' OK.'''
+
Read the message and click ''' OK'''.
 
|-
 
|-
 
||Point to the message.
 
||Point to the message.
Line 453: Line 449:
 
|-
 
|-
 
||Go to the Downloads folder and open '''mgltools_x86_64Linux2_1.5.7''' folder.
 
||Go to the Downloads folder and open '''mgltools_x86_64Linux2_1.5.7''' folder.
−
|| Go to the Downloads directory and open '''mgltools '''folder.
+
|| Go to the '''Downloads directory''' and open '''mgltools ''' folder.
 
|-
 
|-
 
|| Double-click to open '''README''' file.
 
|| Double-click to open '''README''' file.
Line 459: Line 455:
  
 
Scroll down and highlight all the points.
 
Scroll down and highlight all the points.
−
|| Here you will see the '''README''' file. Double-click to open the file.
+
|| Here you will see the '''README''' file.
 +
 
 +
Double-click to open the file.
  
  
Line 465: Line 463:
  
  
−
Scroll down, here you will see how to create''' aliases''' and add them to''' bashrc '''file.  
+
Scroll down.
 +
 
 +
Here you will see how to create ''' aliases''' and add them to''' bashrc '''file.  
  
  
Line 493: Line 493:
  
 
Press''' Enter'''
 
Press''' Enter'''
−
|| Back to the terminal. Let us go back to the home folder,
+
|| Back to the terminal. Let us go back to the home folder.
  
 
type  
 
type  
Line 507: Line 507:
  
  
−
one more time and press Enter.
+
one more time.
  
 
I will now clear the screen.
 
I will now clear the screen.
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alias pmv='sudo /home/username/Downloads/mgltools_x86_64Linux2_1.5.7/bin/pmv'
 
alias pmv='sudo /home/username/Downloads/mgltools_x86_64Linux2_1.5.7/bin/pmv'
−
|| This will open the '''bashrc '''file.  
+
|| This will open the '''bashrc ''' file.  
  
 
Scroll down to the end of the file.
 
Scroll down to the end of the file.
Line 545: Line 545:
  
  
−
Similarly copy the command to create''' alias''' for '''pmv''' and paste it in the '''bashrc '''file
+
Similarly copy the command to create ''' alias''' for '''pmv''' and paste it in the '''bashrc ''' file.
  
 
|-
 
|-
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|| '''AutoDock Tools graphic''' interface opens as shown on the screen.
 
|| '''AutoDock Tools graphic''' interface opens as shown on the screen.
  
−
Close the '''ADT '''interface.
+
Close the '''ADT ''' interface.
  
−
Go back to the terminal and type pmv at the prompt.
+
Go back to the terminal and type '''pmv''' at the prompt.
  
 
press Enter.
 
press Enter.
Line 600: Line 600:
  
  
−
This completes the installation of '''AutoDock''' on '''Ubuntu Linux OS.'''
+
This completes the installation of '''AutoDock''' on '''Ubuntu Linux OS'''.
 
|-
 
|-
 
|| '''Slide Number 8'''
 
|| '''Slide Number 8'''
Line 620: Line 620:
 
|| Created '''aliases '''to use '''AutoDockTools''' (ADT) and '''Python Molecular Viewer''' (PMV).
 
|| Created '''aliases '''to use '''AutoDockTools''' (ADT) and '''Python Molecular Viewer''' (PMV).
  
−
Opened the '''GUI '''for '''ADT''' and '''PMV'''.  
+
Opened the '''GUI ''' for '''ADT''' and '''PMV'''.  
 
|-
 
|-
 
|| '''Slide Number 10'''
 
|| '''Slide Number 10'''
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−
Read information about '''Docking '''given on the page.
+
Read information about '''Docking ''' given on the page.
  
 
|-
 
|-
Line 689: Line 689:
  
 
'''Acknowledgment '''
 
'''Acknowledgment '''
−
|| Spoken Tutorial project is funded by Ministry of Education (MoE), Govt. of India  
+
|| Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India  
 
|-
 
|-
 
||
 
||

Revision as of 12:12, 26 September 2023

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,


Ubuntu Linux OS version 20.04

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,


Basic computer skills and Linux commands.


For the pre-requisite Linux tutorials please visit this website.

Slide Number 6

Files to Download and website link

AutoDock suite v4.2.6

MGL Tools v1.5.7


https://autodock.scripps.edu/

We need to download the following installer files from the official AutoDock website.

AutoDock suite version 4.2.6


MGL Tools version 1.5.7


Open the link shown here in any web browser.

https://autodock.scripps.edu/

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.


Click on AutoDock4 option.

I have opened the AutoDock website.


On the left side of the screen you will see the Downloads link.

Hover the mouse over the Downloads link.


You will see two options.


Click on the AutoDock4 option.

https://autodock.scripps.edu/download-autodock4/


Scroll down the page and highlight the various available installer files.

The page refreshes.


On this page you can see downloadable installer files for Linux, Mac and Windows OS.

Highlight the AutoDock User Manual and Example links.


Click on it to download and save the PDF file.

Scroll down the page.


AutoDock User Manual and Example files are also available.


It is a good practice to download the user manual and go through the examples.


Click on the link to download and save the AutoDock User Manual PDF file.


Similarly, save the Examples file.


The files will be downloaded to your Downloads folder.

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.

Click on the link for MGL Tools.

Back on the downloads page.


We need to also download the MGL tools which include ADT.


Scroll down the page.


There is a message which reads,


To download the graphical user interface of AutoDock Tools (ADT) click here[1]here.


Click on the link.

https://ccsb.scripps.edu/mgltools/


Scroll the page

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.


Type the following command,


cd Downloads


Press Enter.

Cursor in the terminal. Now let us extract and install the files one by one.


For this we will type commands at the terminal prompt.

Slide Number 7


Linux commands for Installing the files

The required commands are provided in a text document in the Additional Materials section.


Please download and save the file.


You can copy and paste the commands from this document.

Show the Desktop folder.

Double-click to open the gedit text file.

I have saved the text file in a folder on the Desktop.


I will open the file in a text editor.

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.


Copy the command as shown, by pressing Ctrl and C keys together.


Paste it in the terminal at the prompt.


Use Ctrl, Shift and V keys to paste the command on the terminal.

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.


Cursor on autodock4 and autogrid files.


Close the folder.

I will double-click on the folder to open it.


You will see two executable files:

autodock4 and autogrid4 in this folder.


Close the folder.

Cursor on the terminal.


Copy the command by pressing Ctrl and C keys together.


Paste it in the terminal at the prompt.


Use Ctrl, Shift and V keys to paste the command on the terminal.

Press Enter.

We will move them to another directory where we keep the binaries.


Open the text document for Linux commands


Copy and paste the commands shown here one by one.


Press Enter to execute the commands.

Cursor on the terminal.


Copy the command by pressing Ctrl and C keys together.

cd x86_64Linux2

sudo mv autodock4 /usr/local/bin

Paste it in the terminal at the prompt.


Use Ctrl, Shift and v keys to paste the command on the terminal.

Press Enter.


Press Enter. Give the system password when prompted.

sudo mv autogrid4 /usr/local/bin

I will copy and paste this command to change the directory.


Copy the next command to move the files to user local bin.


Press Enter.

Give the system password when prompted.

Copy the next command and paste it in the terminal.


Type,


cd press Enter


Type,

cd Downloads


Press Enter.

Come back to the Downloads directory to install the rest of the files.


Type, cd and Press Enter.


Type, cd space Downloads 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.


Paste it at the prompt.


And press Enter.

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,


cd mgltools_x86_64Linux2_1.5.7


./install.sh

Press Enter.

Now to install it, we will go to the mgl tools directory.


Copy the command, paste it in the terminal and press Enter.


cd mgltools_x86_64Linux2_1.5.7


To install I will copy and paste this command.

./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.


Read the message and click OK.

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.


Scroll down and highlight all the points.

Here you will see the README file.

Double-click to open the file.


It shows the paths for running the AutoDockTools and Python Molecular Viewer.


Scroll down.

Here you will see how to create aliases and add them to bashrc file.


Close the README file.

Type

cd ..


Press Enter


Type

cd ..


Type

clear


gedit ~/.bashrc


Press Enter

Back to the terminal. Let us go back to the home folder.

type

cd ..


and Press Enter

type

cd ..


one more time.

I will now clear the screen.


Copy the command from gedit text editor and paste it in the terminal.


gedit ~/.bashrc

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'


alias pmv='sudo /home/username/Downloads/mgltools_x86_64Linux2_1.5.7/bin/pmv'

This will open the bashrc file.

Scroll down to the end of the file.


Copy the following commands from the text editor and paste them in the bashrc file.


Learners please note, use the path which is appropriate for your system.

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.


Similarly copy the command to create alias for pmv and paste it in the bashrc file.

Change the path to

home/snehalatha/Downloads/mgltools_x86_64Linux2_1.5.7/bin/adt'


/home/snehalatha/Downloads/mgltools_x86_64Linux2_1.5.7/bin/pmv'

Save the file.

Change the path in the above command accordingly.


Save the file.

In the terminal type the following command.


source ~/.bashrc


Press Enter.

Go back to the terminal and type the following command.

source ~/.bashrc


Press Enter.

Cursor on the screen.


Type, adt at the prompt. Press Enter.

We have completed the step of creating aliases.


From now on whenever you type adt or pmv it will open them on screen.


Type, adt at the prompt and Press Enter.

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.


This completes the installation of AutoDock on Ubuntu Linux OS.

Slide Number 8

Summary

Let's summarize.


In this tutorial we have,

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,


Explore the Projects tab in the AutoDock website.

Use the link is given below.


https://ccsb.scripps.edu/projects/


Read information about Docking given on the page.

Slide Number 11


About Spoken Tutorial Project

  • The video at the following link summarizes the Spoken Tutorial project.
  • Please download and watch it.


Slide Number 12


Spoken tutorial workshops

  • We conduct workshops using spoken tutorials and give certificates.
  • For more details, please contact us.


Slide Number 13


Answers for THIS Spoken Tutorial

  • Do you have questions in THIS Spoken Tutorial?
  • Please visit this site
  • Choose the minute and second where you have the question.
  • Explain your question briefly
  • The spoken tutorial project will ensure answer.
  • You will have to register on this website to ask questions.


Slide Number 14


Forum

  • The Spoken Tutorial forum is for specific questions on this tutorial.
  • Please do not post unrelated and general questions on them.
  • This will help reduce the clutter.
  • With less clutter, we can use these discussions as instructional material.


Slide Number 15


Acknowledgment

Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
  • This tutorial is contributed by Snehalatha Kaliappan from IIT Bombay.
  • This is Madhuri Ganapathi signing off.

Thank you for joining.

Contributors and Content Editors

Madhurig, Snehalathak

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