Difference between revisions of "AutoDock4/C2/Running-AutoDock/English"

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(Created page with " '''Title of script''': '''Running AutoDock''' '''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar''' '''Keywords: Autodock4, docking, docking parameters, genetic algor...")
 
 
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|| In this tutorial, we will learn to
 
|| In this tutorial, we will learn to
  
−
Open the PDBQT files for receptor and ligand for docking on the ADT interface
+
Open the '''PDBQT''' files for receptor and ligand for docking on the '''ADT''' interface
  
 
Perform docking using default docking parameters
 
Perform docking using default docking parameters
  
−
Save the output as .dpf file.
+
Save the output as '''.dpf''' file
  
 
|-
 
|-
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|| Here I am using,
 
|| Here I am using,
  
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'''Ubuntu Linux '''OS version 20.04
+
'''Ubuntu Linux''' OS version 20.04
  
 
AutoDockTools version 1.5.7
 
AutoDockTools version 1.5.7
  
−
gedit v3.36.2
+
gedit version 3.36.2
 
|-
 
|-
 
|| '''Slide Number 5'''
 
|| '''Slide Number 5'''
  
 
'''Pre-requisites'''
 
'''Pre-requisites'''
−
|| To follow this tutorial you should be familiar with,
+
|| To follow this tutorial learner should be familiar with,
  
 
topics in basic bioinformatics
 
topics in basic bioinformatics
  
−
basic operations on AutoDock Tools interface
+
basic operations on '''AutoDock Tools''' interface
 
|-
 
|-
 
|| '''Slide number 6'''
 
|| '''Slide number 6'''
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|| Save the input files in your home directory or working directory
 
|| Save the input files in your home directory or working directory
  
−
Make a copy of all the files and then use them for practising  
+
Make a copy of all the files and then use them for practising.
  
 
|-
 
|-
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Select '''Macromolecule''' from the dropdown, then select '''Set Rigid Filename.'''
+
Select '''Macromolecule''' from the dropdown, then select '''Set Rigid Filename'''.
  
  
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Select '''2vta.pdbqt''' from the list of files and click on the '''Open '''button.
+
Select '''2vta.pdbqt''' from the list of files and click on the '''Open ''' button.
  
 
|-
 
|-
−
|| click on '''Docking''', from the dropdown choose '''Ligand,''' select '''Open''' option.
+
|| click on '''Docking''', from the dropdown choose '''Ligand,''' and select '''Open''' option.
  
  
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Click on the '''Open''' button.
 
Click on the '''Open''' button.
  
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A pop up window '''AutoDpf4 Ligand Parameters '''appears.
+
A pop up window '''AutoDpf4 Ligand Parameters''' appears.
  
 
Read the information about the ligand.
 
Read the information about the ligand.
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Some default parameters are selected, leave them as such.
 
Some default parameters are selected, leave them as such.
  
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Click on the '''Accept '''button in the pop-up.  
+
Click on the '''Accept ''' button in the pop-up.  
  
 
The pop up window closes
 
The pop up window closes
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Click the '''Accept''' button.
 
Click the '''Accept''' button.
  
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|| Click on '''Docking''' again, from the dropdown choose '''Search Parameters.'''
+
|| Click on '''Docking''' again, from the dropdown choose '''Search Parameters'''.
  
 
From the sub-menu select '''Genetic Algorithm'''.
 
From the sub-menu select '''Genetic Algorithm'''.
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−
We will leave the default parameters as such and click on''' Accept''' button.
+
We will leave the default parameters as such and click on ''' Accept''' button.
 
|-
 
|-
 
|| Click Docking >> Docking Parameters.  
 
|| Click Docking >> Docking Parameters.  
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'''Set Docking Run Options '''window opens.
+
'''Set Docking Run Options ''' window opens.
  
  
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−
We will leave them as such and click on''' Accept''' button.
+
We will leave them as such and click on ''' Accept''' button.
  
 
|-
 
|-
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'''Autodock4.2 GALS Docking Parameter Output File''' dialog box opens.
 
'''Autodock4.2 GALS Docking Parameter Output File''' dialog box opens.
  
−
Type the file name in the '''File name '''field as''' 2vta.dpf'''.
+
Type the file name in the '''File name '''field as ''' 2vta.dpf'''.
  
  
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|-  
 
|-  
 
|| Cursor on '''Run AutoDock''' pop-up.
 
|| Cursor on '''Run AutoDock''' pop-up.
−
|| Here you will again need to set the '''Program Pathname '''and '''Parameter Filename'''.
+
|| Here you will again need to set the '''Program Pathname ''' and '''Parameter Filename'''.
  
−
For me '''Program Pathname''' is already auto populated, hence I will leave it as such.
+
For me '''Program Pathname''' is already auto populated.
 +
 
 +
Hence I will leave it as such.
  
 
Windows users may click on the '''Browse''' button and fill the path for the '''autodock4.exe file'''.
 
Windows users may click on the '''Browse''' button and fill the path for the '''autodock4.exe file'''.
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From the pop-up window, choose '''2vta.dpf''' from the home folder.
 
From the pop-up window, choose '''2vta.dpf''' from the home folder.
  
−
|| '''Parameter Filename '''is also auto populated as '''2vta.dpf.'''
+
|| '''Parameter Filename ''' is also auto populated as '''2vta.dpf.'''
  
  
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−
From the pop-up window, I will choose '''2vta.dpf''' from the home folder.
+
From the pop-up window, I will choose '''2vta.dpf''' from the Home folder.
  
  
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The output file '''2vta.dlg''' will be saved in the home folder.
 
The output file '''2vta.dlg''' will be saved in the home folder.
  
−
We need to open the '''dlg '''file and check the last line to make sure autodock is successfully completed.
+
We need to open the '''dlg '''file and check the last line to make sure '''autodock''' is successfully completed.
  
  
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Scroll to the last line in the document.  
 
Scroll to the last line in the document.  
  
−
Here you will see, '''Autodock4: Successful Completion.'''
+
Here you will see, '''Autodock4: Successful Completion'''.
  
 
Close the text file and close the home folder..
 
Close the text file and close the home folder..
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'''Summary'''
 
'''Summary'''
−
|| Saved the output as .dpf file.
+
|| Saved the output as .dpf file
  
 
Ran AutoDock  
 
Ran AutoDock  
  
−
Opened the .dlg file to make sure the autodock run is successfully completed.
+
Opened the .dlg file to make sure the autodock run is successfully completed
  
 
|-
 
|-
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||Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
 
||Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
 
|-
 
|-
−
|| '''Slide Number 15'''
+
|| '''Slide Number 14'''
  
  

Latest revision as of 11:18, 18 January 2024

Title of script: Running AutoDock


Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar


Keywords: Autodock4, docking, docking parameters, genetic algorithm, dpf file, pdbqt files, dlg file, video tutorial.


Visual Cue Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Running AutoDock
Slide Number 2

Learning Objectives

In this tutorial, we will learn to

Open the PDBQT files for receptor and ligand for docking on the ADT interface

Perform docking using default docking parameters

Save the output as .dpf file

Slide Number 3

Learning Objectives

Run AutoDock

Open the .dlg file to make sure the autodock run is successfully completed.

Slide Number 4

System Requirement

Here I am using,

Ubuntu Linux OS version 20.04

AutoDockTools version 1.5.7

gedit version 3.36.2

Slide Number 5

Pre-requisites

To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on AutoDock Tools interface

Slide number 6

Code Files

The input files required for this tutorial are available in the Code files link.

Please download and extract the files.

Slide number 7

Code Files

Save the input files in your home directory or working directory

Make a copy of all the files and then use them for practising.

Cursor on ADT interface. Here I have opened ADT interface.
Click on Docking on the toolbar.

Select Macromolecule from the dropdown, then click Set Rigid Filename.

Cursor on the panel.

Select 2vta.pdbqt from the list of files. Click on the Open button.

Click on the Docking tool on the menu bar.


Select Macromolecule from the dropdown, then select Set Rigid Filename.


PDBQT Macromolcule File window opens.


Select 2vta.pdbqt from the list of files and click on the Open button.

click on Docking, from the dropdown choose Ligand, and select Open option.


Select ligand.pdbqt from the list of files in the window.

Click on the Open button.

Cursor on the AutoDpf4 Ligand Parameters pop-up window.

Click on the Accept button in the pop-up.

Click on Docking again, from the dropdown choose Ligand, select Open option.

Select ligand.pdbqt from the list of files in the window.

Click on the Open button.

A pop up window AutoDpf4 Ligand Parameters appears.

Read the information about the ligand.

Some default parameters are selected, leave them as such.

Click on the Accept button in the pop-up.

The pop up window closes

Click Docking >> Search Parameters >> Genetic Algorithm.

Cursor on Genetic Algorithm Parameters window.

Click the Accept button.

Click on Docking again, from the dropdown choose Search Parameters.

From the sub-menu select Genetic Algorithm.

Genetic Algorithm Parameters window opens.


You will notice that all the fields are auto populated.


We will leave the default parameters as such and click on Accept button.

Click Docking >> Docking Parameters.

Cursor on the Set Docking Run Options window.

Click the Accept button.

Next click again on Docking and from the dropdown choose Docking Parameters.


Set Docking Run Options window opens.


Again you will notice that all the fields are auto populated.


We will leave them as such and click on Accept button.

Click Docking >> Output >> Lamarckian GA(4.2).


Autodock4.2 GALS Docking Parameter Output File window opens.

Type the file name in the File name field as 2vta.dpf.


The Files of type field is auto populated as dpf file.

Click on Save Button.

To save all the parameters as a single docking file; click Docking again.


Choose the Output option from the dropdown.


From the sub-menu choose Lamarckian GA(4.2).


Autodock4.2 GALS Docking Parameter Output File dialog box opens.

Type the file name in the File name field as 2vta.dpf.


The Files of type field is chosen as dpf file.


Click on Save Button.

Click Run >> Run AutoDock.


Cursor on Run AutoDock pop-up.

Next, Click on Run, Choose Run AutoDock.


Run AutoDock pop-up opens.

Cursor on Run AutoDock pop-up. Here you will again need to set the Program Pathname and Parameter Filename.

For me Program Pathname is already auto populated.

Hence I will leave it as such.

Windows users may click on the Browse button and fill the path for the autodock4.exe file.

Click on the Browse button next to the Parameter Filename field.

From the pop-up window, choose 2vta.dpf from the home folder.

Parameter Filename is also auto populated as 2vta.dpf.


Click on the Browse button next to the field.


From the pop-up window, I will choose 2vta.dpf from the Home folder.


Click on the Open button in the pop-up window.


Now the empty field next to Log Filename will automatically be populated as 2vta.dlg.

Cursor on the cmd field. Here you may also find the command line if you prefer to use the terminal to run autodock4.
Click on the Launch button.

Cursor on Autodock process Manager popup.

Click on the Launch button to run autodock4.

A pop-up titled Autodock Process Manager will appear.

The process time depends on the parameter values you have set.

This will take 10 to 20 seconds.

The pop-up will automatically close when the process ends.

Cursor on the panel. Viewers please note:

If the popup appears and closes quickly within 1 or 2 seconds, an error has likely occurred.

If this happens, check your parameters and run the autodock again.

Cursor on the home folder .

Cursor on output file 2vta.dlg.

Right-click on 2vta.dlg and open it using the text editor.

Open the home folder.

The output file 2vta.dlg will be saved in the home folder.

We need to open the dlg file and check the last line to make sure autodock is successfully completed.


I will right-click and open the file using the text editor.

Cursor on 2vta.dlg document.

Scroll to the last line in the document.

Cursor on Autodock4 Successful Completion.

The file opened in gedit for me.

Scroll to the last line in the document.

Here you will see, Autodock4: Successful Completion.

Close the text file and close the home folder..


This brings us to the end of this tutorial.

Slide Number 8

Summary

Let us summarize.

In this tutorial, we have,

Opened the PDBQT files for receptor and ligand for docking on ADT interface

Performed docking using default docking parameters

Slide Number 9

Summary

Saved the output as .dpf file

Ran AutoDock

Opened the .dlg file to make sure the autodock run is successfully completed

Slide Number 10

Assignment

As an assignment,

Run autodock for the example 1DWD, given in the Examples folder in the Downloads 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 write to us.
Slide Number 113


Forum

  • Please post your timed queries in this forum.
Slide Number 14


Acknowledgement

Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
Slide Number 14


Acknowledgement

This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.

Contributors and Content Editors

Madhurig, Snehalathak

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