In Gentoo Gnome (not sure whether this is a common problem for Gnome) a user can do su (to login as root from a command line) only if they (user) are included to the wheel profile. This can be resolved (by the root) as follows (login the system as root first)

>> gpasswd -a ratna wheel

Here ratna is the user
I ahve doen the following optional profile add as well.
>>gpasswd -a ratna audio
>>gpasswd -a users