On a WHM/cpanel VPS server the httpd.conf is automatically generated from cpanel scripts based on templates and you are not supposed to change this file directly. Any changes that you make in the httpd.conf file will be lost when cpanel re-generates the file or when cpanel is updated. This is an inconvenience especially when your application requires you to make virtualhost modifications in the configuration. However cpanel provides an alternative way to edit the httpd.conf file.