View source for 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.


{|border=1
|| '''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/ 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/ 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.

'''To download the graphical user interface of AutoDock Tools (ADT) click here [https://ccsb.scripps.edu/mgltools/  ][https://ccsb.scripps.edu/mgltools/ click here]'''

Click on the link for '''MGL Tool'''s.


|| 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'''


Click on the link.
|-
||[https://ccsb.scripps.edu/mgltools/ 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 i'''nterface.
|| '''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/ 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. 
|-
|}