AutoDock4/C2/Running-AutoDock/English - Revision history

Snehalathak at 05:48, 18 January 2024

2024-01-18T05:48:56Z

Snehalathak at 05:47, 18 January 2024

2024-01-18T05:47:24Z

Snehalathak at 05:35, 18 January 2024

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Madhurig at 11:33, 17 January 2024

2024-01-17T11:33:57Z

Snehalathak at 06:40, 17 January 2024

2024-01-17T06:40:52Z

Snehalathak: Created page with " '''Title of script''': '''Running AutoDock''' '''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar''' '''Keywords: Autodock4, docking, docking parameters, genetic algor..."

2024-01-17T06:38:57Z

Created page with " '''Title of script''': '''Running AutoDock''' '''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar''' '''Keywords: Autodock4, docking, docking parameters, genetic algor..."

New page

'''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.'''

{|border =1

|| 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 v3.36.2
|-
|| '''Slide Number 5'''

'''Pre-requisites'''
|| To follow this tutorial you 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,''' 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 15'''

'''Acknowledgement '''
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.
|-
|}

@@ Line 28: / Line 28: @@
 Perform docking using default docking parameters
-Save the output as '''.dpf''' file.
+Save the output as '''.dpf''' file
 |-

@@ Line 48: / Line 48: @@
 AutoDockTools version 1.5.7
-gedit v3.36.2
+gedit version 3.36.2
 |-
 || '''Slide Number 5'''
@@ Line 101: / Line 101: @@
 |-
-|| click on '''Docking''', from the dropdown choose '''Ligand,''' select '''Open''' option.
+|| click on '''Docking''', from the dropdown choose '''Ligand,''' and select '''Open''' option.
@@ Line 297: / Line 297: @@
 In this tutorial, we have,
-Opened the PDBQT files for receptor and ligand for docking on ADT interface.
+Opened the PDBQT files for receptor and ligand for docking on ADT interface
-Performed docking using default docking parameters.
+Performed docking using default docking parameters
 |-
@@ Line 305: / Line 305: @@
 '''Summary'''
-|| Saved the output as .dpf file.
+|| Saved the output as .dpf file
 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
 |-

@@ Line 350: / Line 350: @@
 ||Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
 |-
-|| '''Slide Number 15'''
+|| '''Slide Number 14'''

@@ Line 53: / Line 53: @@
 '''Pre-requisites'''
-|| To follow this tutorial you should be familiar with,
+|| To follow this tutorial learner should be familiar with,
 topics in basic bioinformatics
@@ Line 74: / Line 74: @@
 || 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.
 |-
@@ Line 92: / Line 92: @@
-Select '''Macromolecule''' from the dropdown, then select '''Set Rigid Filename.'''
+Select '''Macromolecule''' from the dropdown, then select '''Set Rigid Filename'''.
@@ Line 98: / Line 98: @@
-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.
 |-
@@ Line 118: / Line 118: @@
 Click on the '''Open''' button.
-A pop up window '''AutoDpf4 Ligand Parameters '''appears.
+A pop up window '''AutoDpf4 Ligand Parameters''' appears.
 Read the information about the ligand.
@@ Line 124: / Line 124: @@
 Some default parameters are selected, leave them as such.
-Click on the '''Accept '''button in the pop-up.
+Click on the '''Accept ''' button in the pop-up.
 The pop up window closes
@@ Line 134: / Line 134: @@
 Click the '''Accept''' button.
-|| 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'''.
@@ Line 144: / Line 144: @@
-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.
@@ Line 155: / Line 155: @@
-'''Set Docking Run Options '''window opens.
+'''Set Docking Run Options ''' window opens.
@@ Line 161: / Line 161: @@
-We will leave them as such and click on''' Accept''' button.
+We will leave them as such and click on ''' Accept''' button.
 |-
@@ Line 187: / Line 187: @@
 '''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'''.
@@ Line 208: / Line 208: @@
 |-
 || 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.
+Hence I will leave it as such.
 Windows users may click on the '''Browse''' button and fill the path for the '''autodock4.exe file'''.
@@ Line 218: / Line 220: @@
 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.'''
@@ Line 224: / Line 226: @@
-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.
@@ Line 265: / Line 267: @@
 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.
@@ Line 281: / Line 283: @@
 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..
@@ Line 295: / Line 297: @@
 In this tutorial, we have,
-Opened the PDBQT files for receptor and ligand for docking on ADT interface
+Opened the PDBQT files for receptor and ligand for docking on ADT interface.
-Performed docking using default docking parameters
+Performed docking using default docking parameters.
 |-

@@ Line 24: / Line 24: @@
 || 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
-Save the output as .dpf file.
+Save the output as '''.dpf''' file.
 |-
@@ Line 44: / Line 44: @@
 || Here I am using,
-'''Ubuntu Linux '''OS version 20.04
+'''Ubuntu Linux''' OS version 20.04
 AutoDockTools version 1.5.7
@@ Line 57: / Line 57: @@
 topics in basic bioinformatics
-basic operations on AutoDock Tools interface
+basic operations on '''AutoDock Tools''' interface
 |-
 || '''Slide number 6'''