Thread:Project:Support desk/SpecialPages gives 500 Internal Service Error - Premature end of script headers: php5/reply (5)

Are you using cpanel to manage apache? It probably does its own config system (as suggested by /var/cpanel/templates/apache2/vhost.default ). Consult cpanel's docs.

Additionally there is no requirement the config file be named vhost.conf, that's just a convention. You can also try looking for httpd.conf. Anyhow you should probably consult the documentation that comes with whatever you used to install apache