I have setup DKIM in my google apps for mail signing, when sending mails through GMail interface it signs the mail but when I send a mail through my webserver using SMTP (from CodeIgniter) it doesnt signs the mail.
Can anybody help me what should I do?
Yes, it's actually a server configuration thing. But since you posted on SO, there is also a way to sign the mails manually from within PHP. http://php-dkim.sourceforge.net/
Also had been covered before here: Setting up DomainKeys/DKIM in a PHP-based SMTP client