I am currently using AutoDock for docking my proteins and ligands. I am facing some problems with my step by step procedure (especially in the steps involved in preparing ligand PDBQT file. How to set the number of torsion angles and setting bond as rotatable or non-rotatable?). I am very new in the field of Bioinformatics. It would be very helpful if any one could provide me with a step by step procedure (manual) required for docking in AutoDock. I am working on Windows 7 operating system.
Hello Ghosh
Kindly follow these steps:
Setup receptor PDBQT
1. opened the MGL tool, clicked the ‘File’ option and selected the Read molecule option.
2. selected the protein molecule (protein.pdb) from the Autodock folder.
3. The protein appeared on the screen of the MGL tool.
4. clicked the ‘Edit’ option and selected the hydrogen molecules in order to add them to study the polar interaction.
5. selected the polar option from here.
6. saved the protein as PDBQT in the same Autodock folder.
Set up ligand PDBQT
7. clicked the ‘File’ option again and selected the read molecule and opened the Autodock folder to select the ligand (xylan.pdb)
8. The ligand was visible on the MGL tool window.
9. saved the ligand as PDBQT.
10. saved the ligand in the same folder Autodock.
Set up Grid box
1. clicked the Grid option, selected the macromolecule option and opened the protein molecule (.pdbqt formate) by browsing the Autodock folder.
2. Similarly, clicked the Grid again, selected ‘the set map types’ option and opened the ligand from there.
3. Then clicked the Grid and selected the Grid box option in order to set up a grid box around the molecule.
4. The box along with the parameters appeared on the screen from where the size of the box can be set.
Parameters:
center_x = 31.6
center_y = 24.0
center_z = 12.7
size_x = 74
size_y = 86
size_z = 74
5. saved the grid as GPF in the Autodock folder .By clicking on the Grid from there selected the ‘output’ option and saved as GPF.
6. Then closed the MGL tool.
Perform dockings:
1. pressed window key+R key from keyboard.
2. Then write CMD on open window and pressed.
3. After click on OK button a NEW window called MS DOS prompt opened.
4. In this window wrote docking related commands.
5. gave the C:\program files>dir/p command to read all files of the directory and pressed ENTER key.
6. Then gave the C:\program files>dir/p in order to read the files of program file which contains the folder naming “the scripps research institute” where there the vina.exe was already present.
7. Then pressed ENTER and VINA started to run.
8. Then gave the commands to read the input receptor and ligand pdbqt files.
8. Made a separate folder of the information relevant to the Grid box by the name “config” containing all the sizes and axis. Then I gave the commands to read the config folder.
9. The docking will start and saved result in the .pdbqt formate
Salam
Use this tutorial, it was very useful for me. for beginning left panel its enough.
Thank you Mohamad Akbari for providing the tutorial.
Sincerely
Kavisa Ghosh
You can also watch Autodock vina video tutorial. here, you can perform docking easily step by step.
This can be helpful...
http://www.excli.de/vol12/Shakil_23092013_proof.pdf
I would suggest AutoDock Vina which is more accurate than AutoDock 4.2. and also use LigPlot for the purpose of visualization and use MGL tools to set the grid box.
Mr Telker its true , vina is more accurate than Autodock 4.2 but for modeling 4.2 have more output or descriptor.
I to accept it, Mr Akbari. But some time a manuscript gets rejected because of this which I have experienced. When I communicated the article with 4.2, one of the reviewer said Vina could have been used instead and in addition with few more comments the the article was rejected. I was a coauthor for it.
Absolutely its true.
I like Vina more than 4.2 but 4.2 calculated 8 energy that was good for QSAR,although Vina produce only binding affinity.
thanks for your attention
Hello Ghosh
Kindly follow these steps:
Setup receptor PDBQT
1. opened the MGL tool, clicked the ‘File’ option and selected the Read molecule option.
2. selected the protein molecule (protein.pdb) from the Autodock folder.
3. The protein appeared on the screen of the MGL tool.
4. clicked the ‘Edit’ option and selected the hydrogen molecules in order to add them to study the polar interaction.
5. selected the polar option from here.
6. saved the protein as PDBQT in the same Autodock folder.
Set up ligand PDBQT
7. clicked the ‘File’ option again and selected the read molecule and opened the Autodock folder to select the ligand (xylan.pdb)
8. The ligand was visible on the MGL tool window.
9. saved the ligand as PDBQT.
10. saved the ligand in the same folder Autodock.
Set up Grid box
1. clicked the Grid option, selected the macromolecule option and opened the protein molecule (.pdbqt formate) by browsing the Autodock folder.
2. Similarly, clicked the Grid again, selected ‘the set map types’ option and opened the ligand from there.
3. Then clicked the Grid and selected the Grid box option in order to set up a grid box around the molecule.
4. The box along with the parameters appeared on the screen from where the size of the box can be set.
Parameters:
center_x = 31.6
center_y = 24.0
center_z = 12.7
size_x = 74
size_y = 86
size_z = 74
5. saved the grid as GPF in the Autodock folder .By clicking on the Grid from there selected the ‘output’ option and saved as GPF.
6. Then closed the MGL tool.
Perform dockings:
1. pressed window key+R key from keyboard.
2. Then write CMD on open window and pressed.
3. After click on OK button a NEW window called MS DOS prompt opened.
4. In this window wrote docking related commands.
5. gave the C:\program files>dir/p command to read all files of the directory and pressed ENTER key.
6. Then gave the C:\program files>dir/p in order to read the files of program file which contains the folder naming “the scripps research institute” where there the vina.exe was already present.
7. Then pressed ENTER and VINA started to run.
8. Then gave the commands to read the input receptor and ligand pdbqt files.
8. Made a separate folder of the information relevant to the Grid box by the name “config” containing all the sizes and axis. Then I gave the commands to read the config folder.
9. The docking will start and saved result in the .pdbqt formate
Thank you Sir (Shahid Mahmood). I will follow the steps. For further clarification I will message u.
Sincerely
Kavisa Ghosh
Please watch my step-by-step tutorial on YouTube: https://www.youtube.com/watch?v=4qFUFkC69e8
hello sir,
pls guide me how to initiate docking with auto docker.do we install auto docker and auto docker tool ?
Dear Sandeep Telkar
Please provide the receptor-ligand docking methods for AutoDock Vina. Thank you
these days the scripps.edu site is not opening due to ehich i am not able to download autodock. I habe autodocktools 1.5.6. my problem is I am not getting the scripps research institute directory in my computer, hence not able to find vina.exe
please help me.
can someone send me the vina.exe file ??
Ipsita Roy I have vina.exe. please find attachment.
Thanks
Regards:
Shahid.
Sir Shahid Mahmood
What is the reason behind of selecting the following values in grid size any logic??
center_x = 31.6
center_y = 24.0
center_z = 12.7
size_x = 74
size_y = 86
size_z = 74
I am learning Auto Dock 4.2. I came up to developing PDBQT, .gpg, .dpf files. I struck at developing docking log file (dlg) and .map files. Some commands have to be given, which I need to learn. Let me try. I would be happy, if these two are addressed.
skn
1.A simple click by click protocol to perform docking: AutoDock 4.2 made easy for non-bioinformaticians.
Article A simple click by click protocol to perform docking: AutoDoc...
2. Computational protein-ligand docking and virtual drug screening with the AutoDock suite.
Kavisa Ghosh
https://pdfs.semanticscholar.org/1381/7f541374bd09b720335b054b04bb876f9a32.pdf?_ga=2.188545707.2070633445.1562136852-1435522935.1562136852
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