You'll need a plugin to do so.
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Bukkit is an Minecraft Server Hosting software.
You drag it into the plugins folder. If you want plugins in your minecraft server use bukkit, not the vanilla minecraft server.
you cannot set up permissions in a normal minecraft server. you must have a bukkit server to use permissions. check the bukkit forum for more info.
Minecraft commands were first seen in bukkit server. We do not know when the first commands were made for bukkit servers however
bukkit hamachi or regular? try looking on youtube