In case we are not able to add name servers from WHM, we can add it from shell by using root login information.

Login in to server as root user and run following commands.

root@server[~]#/scripts/adddns domain ns1.your_domain.com ip=111.222.222.1

root@server[~]#/scripts/adddns domain ns2.your_domain.com ip=111.222.222.2

Replace your_domain.com  in above command with your domain name and  use the respective ips which you want to use for your nameservers.
root@server[~]#service named restart
or
root@server[~]#/etc/init.d/named restart

If you require help, contact SupportPRO Server Admin