Remove it from httpd.conf just as it states. Heres some directions.
First you need to open the file in a file editor. Pico is alot easier for newer people. So I always suggest using it. This would be the command to open the file.
pico /usr/local/apache/conf/httpd.conf
Next you need to search through the file and find the lines for the domain in question. You will see lines like the following.
&VirtualHost 1.2.3.4&
ServerAlias www.DOMAIN.com DOMAIN.com
ServerAdmin
[email protected]
DocumentRoot /home/USERNAME/public_html
BytesLog domlogs/DOMAIN.com-bytes_log
User USERNAME
Group GROUPNAME
ServerName www.DOMAIN.com
ScriptAlias /cgi-bin/ /home/USERNAME/public_html/cgi-bin/
CustomLog domlogs/DOMAIN.com combined
ScriptAlias /cgi-bin/ /home/USERNAME/public_html/cgi-bin/
&/VirtualHost&
You want to remove this totally. But make sure you only remove it for the one domain.
So all you need to remove is
&VirtualHost 1.2.3.4&
all the way down to
&/VirtualHost&
Once you remove it hit your control key and O on your keyboard. This will ask you to save the file and overwrite.
Do so and log in to WHM and restart Apache.
This should fix the issue and allow you to create the account. The problem is when you first set up the box you set it to the domain hostname. So it put the stuff in there. Most likely it is set to be looking in /var/www/ I beleive. That's the new default for apache.
On a side note pico has a feature to search files for certain strings. If you wanted to find cpanel.net inside httpd.conf all you need to do is hit control and W on your keyboard. This will ask you for something to search for. Put in cpanel.net and it will find the closet cpanel.net to your current location. Do it as many times as needed to find exactly what you need.
Good luck and I hope these small straight forward directions help you.