Your Autogrid and Autodock executable files (.exe) should be present in your working directory, where you have your pdb and pdbqt files. Also you can specify the path for the files/working directory in the settings in mgl tools.

Try to copy and paste both of these executables in System32 folder of C or your OS hard drive. OR please follow the instructions of Aditya Sharma; however, your commands must be tailored to tell the Autodock cmd to tell where your executable are!

Hi! I had a similar problem where the file could not be found in spite of placing it in the correct folders. I found I was having a problem because of a space character in the path name, which I think in your case would be "Program Files".

Regards, Aditi.

If browsing autogrid doesnt work try to use the command line. Just copy it from the Run tab of ADT (it should be something like this: autogrid4.exe -p grid.gpf -l grid.glg) 

It happens to me in earlier stages. But please try to use command line prompt. I can give you a hint how it works:

OPEN THE FOLDER THAT YOU ARE WORKING SAY venkatesh (YOUR FULL PATH: C:\Users\prashanth\Desktop\venkatesh)

(this can be easily found by 'Right Click in Folder>Properties>Path' . this is very basic and i assume that you know)

CTRL + R (I.E RUN COMMAND)

TYPE cmd

CMD PROMPT WILL OPEN

NOW YOU HAVE TO TELL THE PROGRAM WHERE YOUR FILES ARE LOCATED

just type

cd C:\Users\prashanth\Desktop\venkatesh

Hit ENTER in your keyboard

OK, now we will run autogrid

just type

autogrid4 -p venkatesh.gpf -l anyname.glg

(-l THIS IS SMALL 'L' NOT -1 (MINUS ONE))

HIT ENTER

IF YOU SEE CURSOR BLINKING, THEN CALCULATION IS GOING ON !!! WAIT

AFTER FINISHING GRID,

autogrid4: Successful Completion

Dear Fadare

I hope this comment finds you in good health and spirit.

For running ADT, you should be following next steps:

1- Make sure that if python 2.5 installed on your PC: you can download it from the following URL:

https://www.python.org/download/releases/2.5/

2- install Autodock tools: you can download it at:

http://autodock.scripps.edu/downloads/autodock-4-2-x-installation-on-windows/

3- install mgltools:

http://mgltools.scripps.edu/downloads

After having finished installation of above tools, you can run ADT. Here, I recommend you to following my current protocol for running it:

1- create a workfolder for your job and tag it based on your favorite name. (e.g. project)

2- running ADT in start menu in windows:

after running you should set its directory: following these steps:

a) open ADT> File> Preferences>set> Startup Directory (in this section you should put on your workfolder path and set it). for example: “C:\Users\project

3- prepare ligand and protein in ".pdb" format. Notice, you must labeled them by "Ligand" and "Protein" keywords.

after having finished these steps you can run ADT: Well! you should do the below ways:

1- open ADT:

File > Read Molecule> Select Protein File (“.pdb” file)

Then:

Edit > Hydrogens >Add>>>>>> Polar Only >OK

Edit > Hydrogens> Merge Non Polar >  Continue (in this step if you see any warning please click on "continue")

then:

Edit > Charges > Add Kolman Charges> Ok

File > Save > Write PDB> >Sort Nodes (Check) > OK > (Overwrite) YES

Well! in the next step you should try prepare the ligand:

Ligand > Input > Open> Select Ligand File (“.pdb” file) > OK

Now repeat above steps and then: (in this section you must add charge to your ligand. So, click on Edit menu and:

Edite> Charges> compute Gasteiger

Ligand > Output > Save as PDBQT

******************************

Now you should be executing AutoGrid4:

For run AutoGrid following the below steps:

1-Grid > Macromole > Choose>  Click (Protein) > Select Molecule > OK > save

2-Grid> Set Map types >Choose Ligand> Click (Ligand) > Select Ligand

3-Grid > GridBox> Set the BOX> File > Close Saving Current

4-Grid > Output > Save GPF> grid.gpf> save

5-Run > Run AutoGrid:

a) Select Program Pathname: ‘autogrid4.exe’ (i.e. C:\Program Files (x86) \The Scripps Research Institute\Autodock\4.2.6)

b) Select Parameter Filename: ‘grid.gpf’ (you should select it based on your workfolder path)

c) Launch!

Notice! in this step you must waiting for ADT response. please don't "dismiss" it!

***************************************************************

After having finished above steps following the below ways:

Run ADT:

1)Docking > Macromolecule > Set Rigid filename> Select ‘Protein.pdbqt’ > Open

2-Docking > Ligand > Choose> Click ‘Ligand’ > Select Ligand> Accept

3-Docking > Search Parameters > Genetic Algorithm> Accept

4-Docking > Output > Lamarckian GA> Save file as ‘dock.dpf’

5-Run > Run AutoDock 

A) Select Program Pathname: ‘autodock4.exe’ (C:\Program Files (x86)\The Scripps Research Institute\Autodock\4.2.6)

B) Select Parameter Filename: ‘dock.dpf’ (Based on you workfolder path)

C) Launch!

Please wait for finishing and don't dismiss it!!

***********************************************************

Docking result analysis:

1-Analyze > Docking > Open> Select ‘dock.dlg’ > Open >Assign Ligand New Name > OK

2-Analyze > Macromolecule > Choose> Click ‘Protein’ > Select Macromolecule

3- Analyze > Conformations> Play, Ranked By Energy > Click on the ‘&’ Button

4-Set Play Options >Check ‘Build H-Bonds’> View the hydrogen bonds formed > Check ‘Show Info’> View the Interaction Energy > Build Current Write Complex> Save as ‘Result.pdb’ ” Save....

Now you can see all of your docking results!

This current protocol can help you for running ADT. I hope it was useful for you. Please do not hesitate to contact me if you have any further questions. Otherwise, I hope that we can work together successfully again another time.

All the best,

Hassan

Rasouli H. Hello,

I found your guide extremely helpful. However, AutoDock 4 prompts to insert a .glg file before I can launch AutoGrid and generate the .dlg file needed to start the docking proper. I cannot find the .glg file in my PC. Where do I get or how do I generate it? Thanks in advance!