How to setup the email for a lotus notes server instead of pop3 or smtp?
Take a look at ends of this section http://wiki.openkm.com/index.php/Administring_users
The pop3 configuration now is thinked for automatic importing mails from mail server not from pop3 account user, because it's not good idea be two readers in same account ( who will read first ? we can not be sure about it ). The idea of pop3 accounts is use a general purpose account where users forward or send with cc mails and openkm automatically indexing it ( by some filter conditions ).
