Thank you for your reply sir, i just want to create vacancy so i removed the atom next to the atom2. Is it correct procedure sir, is there any other way.

Removing the atom name will not remove the atom. You have to click the "remove atom" link next to the atom in StructGen. Whether this creates the correct vacancy, I don't not know. You have to determine this yourself. Xcrysden is a good aid, which you can use to help you visualize whether the structure looks reasonable or not.
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