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

Snehalathak at 12:09, 5 September 2024

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Snehalathak at 12:03, 12 January 2024

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Snehalathak at 11:55, 12 January 2024

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Snehalathak: Created page with "'''Title of script''': Running AutoGrid '''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar''' '''Keywords: Autodock4, ADT, ligand, autogrid, macromolecule, pdbqt,''' vid..."

2024-01-11T05:59:57Z

Created page with "'''Title of script''': Running AutoGrid '''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar''' '''Keywords: Autodock4, ADT, ligand, autogrid, macromolecule, pdbqt,''' vid..."

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'''Title of script''': Running AutoGrid

'''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar'''

'''Keywords: Autodock4, ADT, ligand, autogrid, macromolecule, pdbqt,''' video tutorial.

{| border =1
|| Visual Cue
||Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this spoken tutorial on '''Running AutoGrid'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

* Set the grid box parameters
* Create a grid for the receptor molecule
* Save the grid box properties as .gpf file.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* Run the AutoGrid program
* Check the output '''.glg''' file for the successful running of the ''' AutoGrid''' program.

|-
|| '''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

Windows users may use notepad or any other text editor.

|-
|| '''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 file in your home directory or working directory.
* Make a copy of all the files and then use them for practising

|-
|| Open the terminal using “Show Applications” button.

Type '''adt''' at the prompt.

Cursor on ADT interface.
|| Here, I have opened the AutoDock Tools interface.

|-
|| Cursor on the ADT interface.
|| I will open the session saved previously while preparing the receptor for docking.

Please watch the pre-requisite tutorial on preparing the receptor for docking.
|-
|| Click on '''File''' then '''Read Session''',

from the '''Read Pmv Session''' pop-up box, select,

'''2vta-receptor-prep.psf''' file.

Click on '''Open''' button.
|| Click on '''File''' then choose '''Read Session.'''

'''Read Pmv Session''' dialog-box opens.

I will select the 2vta-receptor-prep.psf file which I had saved in my home directory.

Click on the '''Open''' button.
|-
|| Click on '''Grid '''tab on the menu bar.

Click on '''Macromolecule''' and '''Choose''' option.

|| The model of the receptor molecule appears on the panel.

To create the grid, click''' Grid tab '''on the''' '''menu bar.

Select '''Macromolecule''' and click on '''Choose''' option.

|-
|| In the '''Choose Macromolecule''' pop-up box, click on '''2vta.'''

Click on '''Select Molecule '''button at the bottom of the pop-up box.
|| In the '''Choose Macromolecule''' dialog-box click on '''2vta.'''

Click on the '''Select Molecule '''button at the bottom of the dialog-box.
|-
|| Cursor on the pop-up window.
|| A '''WARNING''' pop-up window appears describing the following;

<nowiki>* the number of non-bonded atoms, which ideally should be zero.</nowiki>

<nowiki>* the number of non-polar hydrogen atoms found, and</nowiki>

* Note that the non-polar hydrogens, nphs have been merged.

|-
|| Click '''OK'''

Cursor on pop-up window '''Modified AutoDock4 Macromolecule File.'''

Click on '''Save''' button.

|| Click '''OK''' to close the pop-up.

Another pop-up window '''Modified AutoDock4 Macromolecule File''' opens.

Save the receptor as a .pdbqt file.

We need to use only the '''PDBQT '''file format for creating the grid.

Click on '''Save''' button.

|-
|| Cursor on the '''ADT''' panel.
|| Notice the change in the appearance of the receptor.

The '''gasteiger''' charges are also calculated for each atom.

|-
|| Click '''Grid''' then on '''Set Map Types''',

'''Open Ligand''' option.

In the Ligand File window, select '''ligand.pdbqt''' file.

Click on the Open button.

[https://docs.google.com/document/d/1zjUAaQkwaTQz1TYcASlQH7Pdw35u1jxvYJuJe5ZBKfQ/edit https://docs.google.com/document/d/1zjUAaQkwaTQz1TYcASlQH7Pdw35u1jxvYJuJe5ZBKfQ/edit]

|| Now let us add the ligand to the receptor.

Next click '''Grid''' then on '''Set Map Types''' and '''Open Ligand''' option.

A '''Ligand File''' window opens, select '''ligand.pdbqt''' file and click on '''Open''' button.

|-
|| Cursor on the ADT panel.
|| You can now see that ligand added to the receptor.

On the panel you can see receptor and ligand complex.

|-
|| Cursor on the ADT interface.
|| Next we must prepare the '''grid box '''for this '''receptor-ligand''' complex.

For this we must set the '''grid box''' parameters.

|-
|| '''Slide Number 8 '''

'''About Grid Box '''

[https://www.scripps.edu/sanner/software/adt/Tutorial/AutogpfTutorial.html https://www.scripps.edu/sanner/software/adt/Tutorial/AutogpfTutorial.html]

The grid box set the boundary of the docking.
|| About the Grid Box.

The grid box position defines the region of the receptor where the docking will be performed.

Any region outside the box won't be explored during docking.

|-
|| '''Slide Number 9'''

'''About Grid Box '''

|| However, we must first know the region of the receptor containing the ligand binding site.

Learners must go through the literature for the information on the ligand binding site.

|-
|| '''Slide Number 10'''

'''About Grid Box'''

'''Learners please note:'''

In case we do not know the exact coordinates for grid box, visualize the active site residues and set the grid boxes centering these residues.

A blind docking covering the entire receptor can also be performed.

|| If the active site information is unknown, it is recommended to search all available surfaces.

In such a case the grid box should cover the whole receptor-ligand complex.

|-
|| Click '''Grid > Grid Box'''.

'''Grid Options''' window opens.
|| Back to the ADT interface.

To set the grid box, click on '''Grid '''then select '''Grid Box'''.

'''Grid Options''' window opens.

This will open up a menu-interface with some default options.

|-
|| Cursor on the ADT interface.
|| On the panel you can now see the grid box covering a certain portion of the receptor.

You will need to set the center of the grid as well as the x,y,z dimensions of the grid.

|-
|| Cursor on the ADT interface.
|| Sometimes we may not know the active site information.

In such a case a blind docking covering the entire receptor can also be performed.
|-
|| Rotate the slider towards the right in x, y and z directions to reach 126 points.

Cursor on the receptor-ligand complex.
|| In the Grid Options window, you can rotate the slider in x,y and z directions to cover the entire receptor-ligand complex.

Click and drag the slider towards the right in x, y and z directions.

Drag until you reach maximum capacity 126 points.

As shown here we have the grid box covering the entire protein.

|-
|| Cursor on the ADT interface.
|| In the present example, we already know the coordinates corresponding to the ligand binding site.

|-
|| Rotate the slider towards the right on x, y and z direction to reach 50,

(from 126 points to 50 points)
|| Rotate the slider to change the number of points on x, y and z directions to 50.

Click the slider and drag the mouse from right to left to decrease the number.
|-
|| Cursor on the ADT interface.
|| Observe the grid box, it is now smaller in size.

Also observe that the grid box is not centered on the active site.
|-
|| Change the numbers in the '''Center Grid Box.'''

Change the Coordinates of the center of the binding site in the x, y and z direction to 27.86 , 0.69, 66.23.

'''site-specific docking, '''
|| To center the grid box over the active site, change the numbers in the '''Center Gird Box.'''

Change the coordinates of the center of the binding site in the x, y and z directions.

I will type the numbers in the fields given.

Type 27.86, 0.69, 66.23 in the x, y and z directions.

Here too we can use the slider to change the numbers.

|-
|| Cursor on the ADT interface.
|| Observe the panel, now the grid box is centered on the active site.
|-
|| Click File in the top-left of the '''Grid Options''' window,

choose '''Close saving current.'''
|| To save the grid box properties, click '''File''' in the top-left of the '''Grid Options''' window.

From the options choose '''Close saving current.'''

The''' Grid Options''' window closes.
|-
|| Cursor on the '''ADT''' panel.
|| '''AutoGrid''' requires an input grid parameter file, which usually has the extension ''' .gpf.'''

The grid parameters you just set need to be saved as a .gpf file.
|-
|| Click '''Grid '''on the main on the ADT interface, from the options choose '''Output'''. Select '''Save GPF.'''

'''Grid Parameter Output File''' window opens.
|| Click '''Grid '''on the menu bar on the ADT interface., From the options choose '''Output'''. Select '''Save GPF'''.

'''Grid Parameter Output File''' window opens.
|-
|| Type the file name as '''2vta.gpf.'''

Click on '''Save '''button at the bottom-right in the '''Grid Parameter Output File''' window.

Save the file as '''2vta.gpf.'''
|| Type the file name as '''2vta.gpf.'''

'''Files of type '''field is already autofilled as gpf file.

Click on '''Save '''button at the bottom-right in the '''Grid Parameter Output File''' window.

The file will be saved in your home directory as 2vta.gpf.

|-
|| click on '''Run''' on the toolbar.

Choose '''Run AutoGrid''' from the drop down.

Cursor on '''Run AutoGrid''' window.

|| To run AutoGrid, click on '''Run''' on the menu bar .

Then choose '''Run AutoGrid''' from the drop down.

'''Run AutoGrid''' window appears.

Here you will notice that various fields are auto populated.

|-
|| Cursor on '''Run AutoGrid''' window.
|| Windows users may click on the '''Browse''' button next to '''Program Pathname.'''

They can then choose the location of '''autogrid4.exe.'''

|-
|| Cursor on '''Run AutoGrid''' window.
|| Alternatively, you can copy and paste the '''autogrid4.exe '''file to your working directory.

I am using '''Linux '''hence I will leave it as such as my '''Program Pathname '''is already auto-populated.

|-
|| In the''' Run AutoGrid''' window, Click on the '''Browse '''button next to the '''Parameter Filename''' field.

Select '''2vta.gpf '''from the home folder.

click on the '''Open''' button.
|| Next is '''Parameter Filename.'''

I will click on the '''Browse '''button next to the '''Parameter Filename''' field.

A '''autogrid4 Parameter File''' dialog box opens.

I will select the '''2vta.gpf '''from my home folder and

click on the '''Open''' button.
|-
|| Cursor on the '''Log Filename''' field.
|| '''Log Filename''' field will be automatically populated as 2vta.glg.

Leave the rest of the parameters at the default setting.
|-
|| Click on the '''Launch''' button.

Cursor on the “'''Autodock Process Manager” '''window.
|| Click on the '''Launch''' button.

A popup entitled “'''Autodock Process Manager'''” will appear.

This popup will automatically close when the process ends.
|-
||Open home folder. Cursor on home folder.

Cursor on''' .map''' files.

|| When the popup closes, '''AutoGrid''' has completed the generation of receptor maps.

I will open my home folder and check for a number of files with the extension '''.map. '''

Notice the number of files with '''.map''' extension.

We also must locate the 2vta.glg file.

Learners please note:

Do not delete any of the output files generated during the running of the autogrid program.

These files will be required for the next step, which is running of the autodock program.

|-
|| Cursor on .map files.

Right click on 2vta.glg file, choose, Open with Text Editor option.

Scroll down the pages.

Cursor on the line '''autogrid4: Successful Completion.'''

|| To make sure autogrid is successfully completed, open the .glg file with a text editor.

Right click on the 2vta.glg file and choose, '''Open with Text Editor''' option.

Scroll down the pages to the last line in the document.

Here you can see the message, '''autogrid4: Successful Completion.'''

Close the '''glg''' file.

|-
|| Cursor on the '''.glg file'''.
|| This brings us to the end of this tutorial.

|-
|| '''Slide Number 9'''

'''Summary Slide'''

|| Let's summarize,

In this tutorial, we have,

* Set the grid box parameters
* Created the grid for the receptor molecule
* Saved the grid box properties as .gpf file

|-
|| '''Slide Number 10'''

'''Summary Slide'''

||
* Ran the AutoGrid program
* Checked the output .glg file for the successful running the AutoGrid program

|-
|| '''Slide Number 10'''

'''Assignment'''

|| As an assignment

Run the autogrid for the example, 1DWD given in the Examples folder in the Downloads page.

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

|-
|| '''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 13'''

'''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.

Thank you for joining.
|-
|}

← Older revision		Revision as of 12:09, 5 September 2024
Line 314:		Line 314:

	'''site-specific docking, '''		'''site-specific docking, '''
−	\|\| To center the grid box over the active site, change the numbers in the '''Center ~~Gird~~ Box'''.	+	\|\| To center the grid box over the active site, change the numbers in the '''Center Grid Box'''.

@@ Line 124: / Line 124: @@
 Click on '''Select Molecule '''button at the bottom of the pop-up box.
 || In the '''Choose Macromolecule''' dialog-box click on '''2vta'''.
@@ Line 253: / Line 254: @@
 |-
-|| Click '''Grid > Grid Box'''.
+|| Click '''Grid >> Grid Box'''.
 '''Grid Options''' window opens.
@@ Line 503: / Line 504: @@
 Close the '''glg''' file.
 |-
@@ Line 511: / Line 510: @@
 |-
-|| '''Slide Number 9'''
+|| '''Slide Number 11'''
@@ Line 526: / Line 525: @@
 |-
-|| '''Slide Number 10'''
+|| '''Slide Number 12'''
@@ Line 536: / Line 535: @@
 |-
-|| '''Slide Number 10'''
+|| '''Slide Number 13'''
@@ Line 550: / Line 549: @@
 |-
-|| '''Slide''' '''Number 11'''
+|| '''Slide''' '''Number 14'''
@@ Line 559: / Line 558: @@
 |-
-|| '''Slide''' '''Number 12 '''
+|| '''Slide''' '''Number 15 '''
@@ Line 567: / Line 566: @@
 * For more details, please write to us.
 |-
-|| '''Slide''' '''Number 13'''
+|| '''Slide''' '''Number 16'''
@@ Line 575: / Line 574: @@
 |-
-|| '''Slide''' '''Number 14'''
+|| '''Slide''' '''Number 17'''
@@ Line 581: / Line 580: @@
 || Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
 |-
-|| '''Slide''' '''Number 15'''
+||'''Acknowledgement '''
-−
-−
 '''Acknowledgement '''
 || This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.

@@ Line 280: / Line 280: @@
 Cursor on the receptor-ligand complex.
-|| In the Grid Options window, you can rotate the slider in x,y and z directions to cover
+|| In the Grid Options window, you can rotate the slider in x,y and z directions to cover the entire receptor-ligand complex.
 the entire receptor-ligand complex.

@@ Line 3: / Line 3: @@
 '''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar'''
-'''Keywords: Autodock4, ADT, ligand, autogrid, macromolecule, pdbqt,''' video tutorial.
@@ Line 104: / Line 104: @@
-I will select 2vta-receptor-prep.psf file which I had saved in my home directory.
+I will select '''2vta-receptor-prep.psf''' file which I had saved in my home directory.
@@ Line 281: / Line 281: @@
 Cursor on the receptor-ligand complex.
 || In the Grid Options window, you can rotate the slider in x,y and z directions to cover
- the entire receptor-ligand complex.
+the entire receptor-ligand complex.

@@ Line 181: / Line 181: @@
 Click on the Open button.
 || Now let us add the ligand to the receptor.
@@ Line 212: / Line 210: @@
 '''About Grid Box '''
@@ Line 245: / Line 241: @@
 '''Learners please note:'''
-In case we do not know the exact coordinates for grid box, visualize the active site residues and set the grid boxes centering these residues.
+In case we do not know the exact coordinates for grid box, visualize the active site residues
 A blind docking covering the entire receptor can also be performed.
@@ Line 283: / Line 280: @@
 Cursor on the receptor-ligand complex.
-|| In the Grid Options window, you can rotate the slider in x,y and z directions to cover the entire receptor-ligand complex.
+|| In the Grid Options window, you can rotate the slider in x,y and z directions to cover