Difference between revisions of "AutoDock4/C2/Running-AutoDock/English"
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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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AutoDockTools version 1.5.7 | AutoDockTools version 1.5.7 | ||
| − | gedit | + | gedit version 3.36.2 |
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|| '''Slide Number 5''' | || '''Slide Number 5''' | ||
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| − | || 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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In this tutorial, we have, | 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 |
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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 | ||
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| − | || '''Slide Number | + | || '''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.
|
| click on Docking, from the dropdown choose Ligand, and select Open option.
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.
|
| 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.
|
| Click Docking >> Output >> Lamarckian GA(4.2).
Type the file name in the File name field as 2vta.dpf.
Click on Save Button. |
To save all the parameters as a single docking file; click Docking again.
Type the file name in the File name field as 2vta.dpf.
|
| Click Run >> Run AutoDock.
|
Next, Click on Run, Choose Run AutoDock.
|
| 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.
|
| 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.
|
| 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..
|
| 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 |
|
| Slide Number 12
Spoken tutorial workshops |
|
| Slide Number 113
|
|
| Slide Number 14
|
Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India |
| Slide Number 14
|
This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay. |
