Aslong as it uses standard IMAP/POP3 protocols it should work fine.
Just install it into /var/www/html/atmail
add an alias line in httpd.conf (like /webmail and /suqirrelmail have)
edit the skin to link to atmail (and if you want, remove SM/UM)
(note: if its perl you may need to place it in /var/www/cgi-bin/)
Chris