Plesk’s integration with Apache can be quite confusing for those used to manually modifying the Apache configuration files. It isn’t safe to modify most of the files, because Plesk rewrites them whenever a configuration change is made. Here’s a quick overview of how Plesk fits in with Apache:
The main Apache configuration in /etc/httpd/conf/httpd.conf (or /etc/apache2/apache2.conf on Debian/Ubuntu systems) is left unchanged. It includes /etc/httpd/conf.d/* (or /etc/apache2/conf.d/*). Plesk creates a file in that directory where it does most of its global configuration. That file is generally used for system-wide applications like webmail, mailman, etc. This file is overwritten when certain changes are made via Plesk. It also has an “Include” line for each virtual host like this:
These files contains the VirtualHost configuration for each domain. They also are overwritten whenever certain changes are made via Plesk (and sometimes just at random, it seems). When Plesk is recreating these files, it looks for a corrosponding ‘vhost.conf’ file in the same ‘conf’ directory. If it finds one, then the resulting httpd.include file Include’s that vhost.conf file. in it.
Therefore, if you want to manually make any changes to the Apache configuration for a website, you need to create a vhost.conf file for it, then re-save the domain’s configuration via plesk.
Also, if you’d like to bypass the whole plesk ordeal for a new domain, you can still create the Apache configuration manually in the original /etc/httpd/conf/httpd.conf file (or /etc/apache2/sites-available/* files).