Its getting difficult to notice if any wrong port is still open or some web server is out of date
This isn't generally done with security scanners unless you're running hundreds of nodes. Use iptables rules with inclusive rules only to block ports. Keep your software inventoried for the rest, or some sort of basic configuration management.
If you don't have these basics, what good is a scanner going to do for you?
E: Re-reading this, I didn't mean for it to sound snide. Genuinely wanting to help .... OpenVAS is probably what you're after.