Dear Sanjay!

Well. I agree with Mr. Alberti comments. Yes, ‘Cygwin’ has HELP to create the Linux environment in Windows. Last one-and-half, I'm using this AutoDock program. Beginning of my work, I had done in Windows platform only. I'm also facing similar issues. From my experience, I could like to share one more tips, you try to keep the following files in your working folder

1. AD4_parameters.dat

2. AD4.1_bound.dat

3. autodock4.exe

4. autogrid4.exe

What are these files? How to get these? (see the attachment-screenshot)

AutoDock program has making many issues in Windows platform. Is my opinion you better to select Linux platform for AutoDock work (especially, Ubuntu & Linux Mint versions are good)

You may also try AutoDock vina, PyMOL vina plug-in. It’s easier to work compared with this

AutoDock Vina: http://vina.scripps.edu/index.html

PyMOL vina plug-in: http://wwwuser.gwdg.de/~dseelig/adplugin.html

I hope is may HELP you.

Thanks

Hey pal... Thanks for your reply, actually I was following the same tutorial.... But at the end I am facing the problem I have written.....

Dear Sanjay,

Check your map files, maybe your PDB structure contains some strange atom type (like some undefined metal ions) then rerun Autogrid 4 to creating new map files.

Hope it helps.

HAH

Dear Sir,

Thank you for your kind and nice reply. Actually my pdb structure is a modelled structure hence is not having any strange molecule, neither water nor it is having any sort of metal ion or anything. but still I am not getting the Map files created.

Can you please tell me which are the files I should put together in a single file, and where should store them. I am always asked by my system about the confirmed modification of the directory since it is in C drive. and I have tried to run it at least 5 times but it is making any grid point map files. and hence reports that pdbqt file not detected.

In case you have any tutorial for windows, then please attach it below.

First, remove windwos, second install linux, then proceed as if under linux ;-)

I have done that. But problem was the same of map files.

Dear Sanjay,

I’ve been using autodock just to try docking some ligands with my enzyme. I think you could try to install Cygwin, and run the autogrid and autodock programs with Cygwin. I don't have many skills with autodock, nor bioinformatics, but it seems to work for me. I'm running Autodock 4 on a computer with Windows XP.

You may find this tutorial useful too :

http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf

I hope this will help you!

J.C. Alberti

Dear Sanjay!

Well. I agree with Mr. Alberti comments. Yes, ‘Cygwin’ has HELP to create the Linux environment in Windows. Last one-and-half, I'm using this AutoDock program. Beginning of my work, I had done in Windows platform only. I'm also facing similar issues. From my experience, I could like to share one more tips, you try to keep the following files in your working folder

1. AD4_parameters.dat

2. AD4.1_bound.dat

3. autodock4.exe

4. autogrid4.exe

What are these files? How to get these? (see the attachment-screenshot)

AutoDock program has making many issues in Windows platform. Is my opinion you better to select Linux platform for AutoDock work (especially, Ubuntu & Linux Mint versions are good)

You may also try AutoDock vina, PyMOL vina plug-in. It’s easier to work compared with this

AutoDock Vina: http://vina.scripps.edu/index.html

PyMOL vina plug-in: http://wwwuser.gwdg.de/~dseelig/adplugin.html

I hope is may HELP you.

Thanks

Thank You Sir Alberti and Sir Mani Maran for your valuable suggestions, Let me try these.

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...