Using ADT on windows is bit problematic, there are some points to consider when using ADT on windows.

1- Make sure there are no spaces in names of files/folder/directory which you are using for docking experiments. (your directory has space in "ADT Workspace" you can change the spaces with _ underscore.

2- Before running autogrid, you can select maps according to your ligand type, from Grid - Set Map Types - Choose Ligand and then selecting your ligand.

3- Copy the Autodock4 and Autogrid4 executable files from installation directory of Autodock4 into your working directory and choose the appropriate files when running autodock or autogrid.

Hope this helps

Talha Islam I was able to run the autogrid and got the map files but am getting the below error in running autodock now.

Sahil Lohana , I think your working directory lack the .dat files required for MGL tools to work. You can find these two files in, MGL tools installation Directory, typically it is located as C:\Program Files (x86)\MGLTools-1.5.7, from there you can go into Lib folder and from there site-packages, and then click on AutoDockTools folder, you will find two files named as 1- AD4.1bound.dat and 2- AD4_Parameters.dat, copy these two files into your working directory and run the autodock again, hopefully it will work.

The full directory for these two dat files will look similar to following,

C:\Program Files (x86)\MGLTools-1.5.7\Lib\site-packages\AutoDockTools

Talha Islam Thank you for your answer! I was able to get the autodock to work!

I have been looking online but cannot understand how to label the binding sites of my receptor where my ligand is bonded to it.

There is so much space between the receptor and the ligand visually, I am not sure if it has even bonded together.

Sahil Lohana You can use programs like Discovery Studio Visualizer, LigPlot+, PyMol and others to see the interactions of your ligand with the macro-molecule. Your Docked ligand seems fine. I would advice you to convert both the receptor and docked ligand pose into mol2 or pdb format and then run the post docking analysis on any software like I mentioned earlier in this answer. There are many videos on youtube which will show you how to run post docking analysis to study the interactions. Best of Luck!

Talha Islam Thankyou for your answer!

I already tried saving it as a pdb but autodock says that 'The current section contains more than one molecule' and gives me an eroor.

Sahil Lohana in MGL Tools, you can write the whole complex as a single file when you are going through docking analysis (through Analyze tab). However, you can also save each molecule (Receptor and Ligand) individually through MGL Tools by opening them one at a time. There are also other tools available like OpenBabel (GUI and Command line versions) which you can use to convert the files from one format into another. I would suggest you to read documentation for MGL Tools about analyzing results and saving complex file or watch Youtube videos about Autodock results analysis in MGL Tools. Hope this helps.