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I have a web application that sends email connecting to localhost as the SMTP. The SMTP is using send mail. My configuration was working fine where all emails to *@mydomain.com where handled by google apps for domain. My VPS was rebooted and now if the app tries to send emails to *@mydomain.com it ends up in my root email box on the vps (not gmail). If I send to the same address from outside the server all works fine.

I know I was messing with some host settings a few weeks ago and I think after the reboot SOME setting took effect and now sendmail things mydomain.com should be handled locally. Any ideas what setting I might have messed up?

hostname still shows vps.server.com (not my domain).

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Try running 'sendmail -bt' and entering '$=w' on prompt shown. It should print list of domains which sendmail recognizes as local. –  AlexD Jun 14 '11 at 16:38
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If you are indeed running sendmail and not postfix or qmail (they both provide a binary named sendmail for compatibility reasons) then this blog post might be of help.

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