Hi Ph_Noha,

Check the following ResearchGate archive:

https://www.researchgate.net/post/how_to_rectify_error_in_autodock

Well if you have a linux system then you can install autodock on it and then you can go to my profile and find out a script specially for autogrid calculations.

If not, then go to your home directory and see if the package has all the components or not; i.e., re-install your autodock.

i intalled it again Anwesh and the folder contains autodck, autogrid and cygwin

is there something else missing?

It is not clear how you are issuing command to run autogrid4.exe. Are you running autogrid4.exe through cygwin terminal? You can try running the autogrid4.exe from windows command prompt. Hope you have made protein.gpf as per the autodock docking protocol. Check following things before running autogrid and revert back with the error if any.

1. The folder contains protein.gpf

2. Folder contains ligand.dpf (not required for autogrid though)

3. Folder contains autogrid4.exe and autodock4.exe

4. Try keeping AD4.1_bound.dat and AD4_parameters.dat files in this folder. (Find these in the C:\Program Files\MGLTools-1.5.6\Lib\site-packages\AutoDockTools)

5. Run the autogrid4.exe from windows command prompt by going to this folder and the command-

>autogrid4.exe -p proetin.gpf -l protein.glg

Revert back if still the error message flags.

Best of luck.

Cygwin is required to creat linux like environment in windows. As you have installed autodock on windows system, cygwin is not required. (For autodock vina it can be used to run some bash scripts for virtual screening purpose).

So try windows command prompt to run autogrid4.exe and autodock4.exe.

Now again execute the autogrid by either command prompt or via visual mode; i.e., by clicking on the icons you would see that at the end a command line is generated; now you copy this command line and then paste it to your terminal, perhaps this could work or simply execute the command from the visual mode by clicking run. And there you would be able to notice if all the files, etc. are present in the working directory or not.

I would personally suggest you to work on linux, as the scripting in linux saves a lot of time as well as the error, if any, is detailed sufficiently.

Hope it helps. Good luck.

when I try to run autogrid then launch box appears and then disappear suddenly. what is the reason for that

Its showing error like file not found i

Hi Noha

Please make sure protein pdbqt file does not contain any space. You have to write protein.pdbqt. it will definately help you out from this problem.

Ms Radhika

In Autidock, open grid option,

Then choose macromolecule, once macromolecule open then choose set map type - choose directly than a box open tahn simply right F in to this box and click on accept. Then follow the same procedure which you used to create gpf file. I also attached two images please refer that.