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

Title Slide

Learning Objectives

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.

Learning Objectives

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

System Requirement

Ubuntu Linux OS version 20.04

AutoDockTools version 1.5.7

gedit v3.36.2

Pre-requisites

topics in basic bioinformatics

basic operations on AutoDock Tools interface

Code Files

Please download and extract the files.

Code Files

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

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.

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.

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.

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

Cursor on Genetic Algorithm Parameters window.

Click the Accept button.

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.

Cursor on the Set Docking Run Options window.

Click the Accept button.

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.

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.

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.

Cursor on Run AutoDock pop-up.

Run AutoDock pop-up opens.

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.

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

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 Autodock process Manager popup.

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.

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 output file 2vta.dlg.

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

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.

Scroll to the last line in the document.

Cursor on Autodock4 Successful Completion.

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.

Summary

In this tutorial, we have,

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

Performed docking using default docking parameters.

Summary

Ran AutoDock

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

Assignment

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

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Acknowledgement

Acknowledgement