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You can enable and disable webmail applications as per user accounts.
Suppose the username is xyzco for your domain xyz.com, first login to SSH into the server as root, and edit the file mentioned below:
pico /var/cpanel/users/xyzco
Now, if you want to disable all webmail applications and enable roundcube mail, you would need to add following lines:
skiphorde=1
skipsqmail=1
skiprcmail=0
Next, you'll need to restart cPanel, you can normally do this by doing :
/etc/init.d/cpanel restart
Now, when the user xyzco logs into webmail, they only see roundcube mail, and not the other two.
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