First you should get the grid center coordinate, i.e. pick up in the pdb file the coordinates of the center atom of your motif. Then run autogrid with this coordinate in your input script.

Thanks for the reply. How to find out the center atom?

you have to make a choice. Ideally based on experimental data.

Do we have any online software which can get me the coordinate, which i may define it in autodock?

Give a try to autodock tools.

i have tried autodock, it demands grid coordnates.. This is what the problem is :(

Try to create grid on the basis of coordinates of active site of protein

"autodock tools" is a separate program.

Going through the tutorials would sound reasonable:

http://autodock.scripps.edu/faqs-help/tutorial

Dear Chawla,

Initially try to translate and rotate the protein and find your motif or active site. In defining the grid box, you can see "pick an atom" or "Center on atom" something like this at the top of the grid dialogue box. Now you can adjust the spacings in x, y and z direction so as to construct a reasonable box. Finally, don't forget to click "Close saving current selection" . Bye

Thank you for the reply prashanth, i will try this option