i typed one ICAO code into the POS INIT page. And there goes its coordinate. But if i typed a gate number of that airport it shows NOT IN THE DATA BASE I tried a lot of airports. the problem remains. So, how can i manually modify FSX files to add gates coordinates?

You might try the scenery design forum for that one. Sometimes it's just a matter of knowing exactly how that gate number should be entered.

The sidstar file must have the gates included, and even then I haven't played with the NGX to see if it will use that. For sim purposes, it's better to use the MSFS coordinates I think.

Why you want to use the Gate coordinates of the Airport??, if you have the GPS coordinates on the POS REF page. Most airlines I know don't even use the gate coordinates in the NAV DATA base to ALIGN the IRS system. Most pilots always uses the GPS coordinates because that is most accurate.