I am writing this post after seeing a query in a forum. The procedure to create custom keyboard shortcuts is
1) Open Gnome configuration editor goto apps–> metacity –>keybinding_commands
2) Double click on command1 and enter the program you want to add shorcuts for. In this example we take gnome-calculator and press ok button.
3) Then goto apps>metacity–> global keybindings
4) Double click the key run_command1 and enter the key bindings. Suppose we want to give it as Alt+c. Type as c in the field and press ok button.
Thats all !!. Now close the configuration editor and press alt+c. You will see the gnome-calcultator appearing on your screen.