It may be that the paths have not been defined correctly. When the "Run AutoGrid" wizard opens, check to ensure that the Working Directory and file names and paths are correct; if not, correct them through Browse button, not by hand. As an additional point to say, MGL-tools works better in Linux than in Windows.

Autodock Vina is a faster and somewhat more accurate tool than AutoDock. If you use it in correct way, surely you'll give a reliable result.

The menu option Grid > Edit GPF helps you edit the gpf file (use Write button to save).

Important values in the gpf file are set in previous steps when you define the ligand, receptor, grid box and when generating the map files. Additional settings are not usually required; defaults are OK in many cases.

Agree with Ebrahim. I always keep receptor and ligand pdbqt files with in the same folder with grid or docking configuration files. Although I hate using mouse, I have to choose receptor and ligand again and again for grid and docking parameter generating.

Thanks for suggestion, I am using linux 12.04lts. so I can open ADT from terminal after entering my working folder. In my working folder I kept all files like ligand.pdbqt , protein.pdbqt, and gpf files. I am following "autodock4 and autodock vina with autodocktools" tutorial , in this tutorial I faced problem from chapter AD4-Exercise Six: Starting AutoGrid4 page no-13. I  am attaching the file. So please give me suggestion to over come from this problem.

Still I think it's nothing more than a problem in defining the paths. Set your current working folder as the startup directory:

File > Preferences > Set > General > Startup Directory > type-in the path of the corresponding folder > Set > Make default

This way you define a sort of unified path for all AutoDock tasks; it may help.

Dear and Respected researcher and Scientists,

I am doing molecular docking studies in this study CYGWIN _I not working properly .

The following command not running tail -f 2fum.glg

Hence i kindly request to you rectify this problem.

Thanks

@Palaniyandi The image is unclear. It seems you have a syntax error, i.e. a space is required between -l and the filename. Otherwise it may be that the path to your autogrid executable is not defined.

Thank you very much sir for your valuable answer and suggestion , but i given all the command , i have problem tail command ,it is not supported, if You not mistaken me , i will send my all the files to you u can run and tell to me sir where i did mistake.

Dear Chandramouli Ghosh,

Hope it is not too late and Sorry if i missed anything in the above discussion as i didnt go through all the answers. Looking at your screen shot i can suggest you to use autogrid4 and autodock4 and not autogrid4.exe and autodock4.exe (remove the exe extension and try).

Autogrid4 -p name.gpf -l name.glg

Autodoc4 -p name.dpf -l name.dlg