I have bought the VPS it gives me 500 server error when ever I create new account on it and try to access it using the http://IP:~username. It does not shows index files and directories.
Go check the apache error log, /usr/local/apache/logs/error_log or go one of the domain`s cpanel and check the error log from there.
Yes, It worked only when I use the first line of .htaccess file as Options +Indexes But I need to add that line whenever I create the new account. It is not possible for me all the time to check and solve it.
If that is the case, it could be because you do not have an index document for that URL. If it could list files / directories in that URL when using Options +Indexes, then you probably should try putting an index file in that folder and see what happens.
Yes when I put index file it works but I am uable see the directory when I use http://IP:~username format to check the account.
Or last try using the following step in your WHM panel go to the check Directory '/' Options at Main >> Service Configuration >> Apache Configuration >> Global Configuration. Indexes and all options are checked.