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Different SSL VPN products work in different ways. Some SSL VPN products proxy incoming SSL sessions to native protocol sessions with internal servers. Other SSL VPN products use SSL as a generic tunneling protocol, port-forwarding anything that arrives over the tunnel to the internal server. Your ability to use native applications and ports depends on the type of SSL VPN product that you use.
For example, if you're using an SSL VPN proxy, it may not be designed to support native e-mail client applications at all. Instead, it may be necessary to use a web portal interface to reach your e-mail server through the SSL VPN gateway. In this case there is no e-mail client reconfiguration necessary -- you simply use your browser as your e-mail client. The SSL VPN gateway is then configured to send e-mail to the port your e-mail server expects -- that is, the gateway can send plain old POP3 (110) and IMAP (143), or you can send POP3S (995) and IMAPS (993).
If you're using an SSL VPN that port-forwards native protocols over SSL, you'll probably need to reconfigure your e-mail client to send outbound traffic to localhost instead of the destination e-mail server. The SSL VPN agent running on the local host will intercept e-mail traffic and forward it over the SSL tunnel. Upon receipt, the SSL VPN gateway will forward that e-mail traffic on towards the e-mail server. In this case, whatever port the e-mail client sends traffic through will be the port the e-mail server receives traffic on.
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