Rules about changing Apache configuration on Godaddy VPS servers are as follows.

1. you can NOT change the original configuration file /etc/apache2/conf/httpd.conf, since this file is autogenerted.

2. You can only change the specific three files

/etc/apache2/conf.d/includes/pre_main_global.conf
#       /etc/apache2/conf.d/includes/pre_virtualhost_global.conf
#       /etc/apache2/conf.d/includes/post_virtualhost_global.conf

You can two methods to modify the above three files.

Method 1, on terminal

Method 2, on Godaddy WHM page

Server Configuration / Apache Configuration / Include Editor