I have a problem with my current VPS server running CentOS 6 and is managed with WHM and cPanel. All my websites were being created from WHM and are located in the /home directory (ownership: mysite:mysite owns mysite/)
Recently, I ran a permission fix to make sure all the sites are being owned by the correct users and user groups. The script that I used to run the fix is: https://knowledgebase.servint.net/questions/674/A+Script+for+Fixing+File+Permissions
After running the fix, my sites are not accessible anymore though I'm not sure what is wrong here. It's even more weird because I can still perform other actions such as ssh'ing to the server, logging in the WHM and site's cPanel (so not a firewall issue) - it is just only the site itself that can't be accessed (not found error).
I highly doubt that this is something wrong with the DNS setting. However, I did check the DNS Zone Editor within one of my sites' cPanel and it still got it correctly.
So now I have no idea how to fix it. Any help/guess is very much appreciated.