Sometimes named.conf got corrupted in cPanel server, To fix that issue follow the steps below:
First of all move the corrupted named.conf using the below command :
mv /etc/named.conf /etc/named.conf-corrupted
Now simply execute the cPanel script to rebuild the named.conf :
/usr/local/cpanel/scripts/rebuilddnsconfig
Restart the named service :
/etc/init.d/named start
Everything should be fine now.