Difference between revisions of "AutoDock4/C2/Installation-of-AutoDock4-on-LInux-OS/English"
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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 47: | Line 47: | ||
Ubuntu Linux OS version 20.04 | Ubuntu Linux OS version 20.04 | ||
− | AutoDock version 4 .2.6 | + | AutoDock version 4.2.6 |
MGL Tools version 1.5.7 | MGL Tools version 1.5.7 | ||
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 | + | The files will be downloaded to your '''Downloads''' folder. |
|- | |- | ||
Line 156: | Line 156: | ||
Scroll down the 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. | Click on the link for '''MGL Tool'''s. | ||
+ | |||
+ | |||
|| Back on the downloads page. | || Back on the downloads page. | ||
− | 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 174: | ||
− | '''To download the graphical user interface AutoDock Tools (ADT) click | + | '''To download the graphical user interface of AutoDock Tools (ADT) click here''' |
Line 179: | Line 183: | ||
Scroll the page | Scroll the page | ||
− | || You will be | + | || 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 199: | ||
|- | |- | ||
||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 206: | ||
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 ''' | + | 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''' | ||
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|- | |- | ||
||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. |
|- | |- | ||
|| Type, | || Type, | ||
− | '''cd Downloads''' | + | '''cd Downloads''', Press '''Enter'''. |
− | + | ||
− | Press '''Enter'''. | + | |
|| We have downloaded all the installers to the '''Downloads''' directory. | || We have downloaded all the installers to the '''Downloads''' directory. | ||
Line 241: | Line 243: | ||
Press''' Enter.''' | Press''' Enter.''' | ||
|- | |- | ||
− | || | + | ||Cursor in the terminal. |
− | + | || Now let us extract and install the files one by one. | |
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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 | + | || 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 287: | ||
− | 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 334: | ||
− | Press '''Enter '''to execute the | + | Press '''Enter ''' to execute the commands. |
|- | |- | ||
|| Cursor on the terminal. | || Cursor on the terminal. | ||
Line 339: | Line 341: | ||
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 354: | ||
Press Enter. Give the system password when prompted. | 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. | Copy the next command to move the files to user local bin. | ||
− | |||
− | Press '''Enter'''. Give the system password when prompted. | + | Press '''Enter'''. |
+ | |||
+ | Give the system password when prompted. | ||
Copy the next command and paste it in the terminal. | Copy the next command and paste it in the terminal. | ||
− | |||
− | |||
− | |||
Line 379: | Line 382: | ||
− | Press Enter | + | Press '''Enter'''. |
− | || Come back to the | + | || Come back to the '''Downloads''' directory to install the rest of the files. |
− | Type, | + | Type, cd and Press '''Enter'''. |
− | |||
+ | Type, cd space Downloads | ||
− | + | Press '''Enter'''. | |
− | + | ||
− | + | ||
− | + | ||
|- | |- | ||
|| Copy the command | || Copy the command | ||
Line 400: | Line 400: | ||
|| Back to the text document. | || Back to the text document. | ||
− | Copy the command to extract '''mgl '''tools. | + | Copy the command to extract '''mgl ''' tools. |
− | Paste it at the prompt | + | Paste it at the prompt and press Enter. |
− | + | ||
− | + | ||
− | + | ||
|- | |- | ||
||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''' | + | || This will create a folder in your '''Downloads''' directory as shown here. |
|- | |- | ||
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Copy the command, paste it in the terminal and press Enter. | Copy the command, paste it in the terminal and press Enter. | ||
− | |||
− | |||
− | |||
Line 437: | Line 431: | ||
|- | |- | ||
||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 447: | ||
|- | |- | ||
||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 453: | ||
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 461: | ||
− | Scroll down | + | Scroll down. |
+ | |||
+ | Here you will see how to create ''' aliases''' and add them to''' bashrc '''file. | ||
Line 493: | Line 491: | ||
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 505: | ||
− | one more time | + | one more time. |
I will now clear the screen. | I will now clear the screen. | ||
Line 528: | Line 526: | ||
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 536: | Line 534: | ||
− | Learners please note | + | Learners please note the path which is appropriate for your system. |
As mentioned earlier, you may find the path in the '''README''' file. | As mentioned earlier, you may find the path in the '''README''' file. | ||
Line 545: | Line 543: | ||
− | 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. |
|- | |- | ||
Line 569: | Line 567: | ||
Press Enter. | Press Enter. | ||
|| Go back to the terminal and type the following command. | || Go back to the terminal and type the following command. | ||
− | |||
− | |||
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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 596: | ||
− | 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 616: | ||
|| 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''' | ||
Line 636: | Line 632: | ||
− | Read information about '''Docking '''given on the page. | + | Read information about '''Docking ''' given on the page. |
|- | |- | ||
Line 689: | Line 685: | ||
'''Acknowledgment ''' | '''Acknowledgment ''' | ||
− | || Spoken Tutorial project | + | || Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India |
|- | |- | ||
|| | || |
Latest revision as of 17:31, 27 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,
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,
|
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
|
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.
|
I have opened the AutoDock website.
Hover the mouse over the Downloads link.
|
https://autodock.scripps.edu/download-autodock4/
|
The page refreshes.
|
Highlight the AutoDock User Manual and Example links.
|
Scroll down the page.
|
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.
|
Back on the downloads page.
|
https://ccsb.scripps.edu/mgltools/
|
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.
|
Cursor in the terminal. | Now let us extract and install the files one by one.
|
Slide Number 7
|
The required commands are provided in a text document in the Additional Materials section.
|
Show the Desktop folder.
Double-click to open the gedit text file. |
I have saved the text file in a folder on the Desktop.
|
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.
|
I will double-click on the folder to open it.
autodock4 and autogrid4 in this folder.
|
Cursor on the terminal.
Press Enter. |
We will move them to another directory where we keep the binaries.
|
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.
|
Type,
cd Downloads
|
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.
|
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.
|
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.
|
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.
|
Type
cd ..
cd ..
clear
|
Back to the terminal. Let us go back to the home folder.
type cd ..
type cd ..
I will now clear the screen.
|
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'
|
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.
|
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.
|
In the terminal type the following command.
|
Go back to the terminal and type the following command.
|
Cursor on the screen.
|
We have completed the step of creating aliases.
|
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.
|
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.
|
Slide Number 11
|
|
Slide Number 12
|
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Slide Number 13
|
|
Slide Number 14
|
|
Slide Number 15
|
Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India |
Thank you for joining. |