The problem can be from the initial files that you prepared for the docking. Have you prepared the ligand and protein using the Autodock tutorial?

yes dear, I have prepare all the required files as required. I have now a pdbqt file of the protein, a pdbqt file of the ligand and an out file, what to do next, i dont know. can you guide me accordingly.

open your result with notepad or same software !

If your result has problem . you can see

Dear Huma Naveed,

Thank u so much for answer, I will try it. Can u help me if the problem still remains there?

well khan what you have to do is simply select the first model from the generated pdbqtout file and paste that model at the end of your original pdb of protein...

You have to paste HETATOM after "Ter" and before "END". Now load that protein in vmd and perform calculations what you want.....

one thing you should remove default HETATOMS (if any exist) from your protein's pdb...

Hopefully it would be beneficial