Following is the output

anjum@anjum-laptop:~$ sudo nvidia-xconfig
[sudo] password for anjum:

Using X configuration file: "/etc/X11/xorg.conf".

WARNING: No Layout specified, constructing implicit layout section using screen
"Default Screen".


WARNING: Unable to find CorePointer in X configuration; attempting to add new
CorePointer section.


WARNING: The CorePointer device was not specified explicitly in the layout;
using the first mouse device.


WARNING: Unable to find CoreKeyboard in X configuration; attempting to add new
CoreKeyboard section.


WARNING: The CoreKeyboard device was not specified explicitly in the layout;
using the first keyboard device.

Backed up file '/etc/X11/xorg.conf' as '/etc/X11/xorg.conf.backup'
New X configuration file written to '/etc/X11/xorg.conf'

anjum@anjum-laptop:~$

please advice.

Well, you got a few warnings. So?

In other words, do you have a problem that needs a solution? Does the new xorg.conf fail to work?

'nvidia-xconfig' cannot write a new file, just modify,
AFAIK.

An '/etc/X11/xorg.conf' for a modern Xorg is almost
empty ( or missing ) so you might have to write a new
one, if you haven't got a backup from earlier installs.

I can see on my Ubuntu 8.10, that the file is from
PCLinuxOS. It can be generated with a live cd and
saved to usb-key or to Google Docs. Uncomment line
30, # Load "freetype" for use in Ubuntu.
....

Do note the last line in the output provided by the OP:So, unless you meant "Can not create an xorg.conf file when one does not already exist," the evidence seems to contradict your assertion. And I believe (but I've not checked) that, even if you renamed your xorg.conf before running the nVidia application, you'd still get a new xorg.conf created.

In any case, all the OP has is a few warning messages of no significance that I can see, and, as I said in my first post, there is no report of any problem on the system.