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What DE are you using? Different DEs handle VNC differently if you're using Wayland as opposed to X11.

Also, what exactly don't you know that you would need to know to run the server without a GUI? If you already know how to SSH and start the server that way (or better idea -- create a systemd service for it (I can show you how to do that)) and you just need to launch the server without a head attached, just modify your startup script to do java -jar minecraft_whatever_server.jar nogui. If you want to run Minecraft commands from the server console while headless, you can type them directly into the terminal while the server is running. If you set up the Minecraft server with systemd, you won't have a terminal, so I'd recommend using Rcon/mcrcon instead. It's built into the vanilla server and not too tough to set up. I'll show you how if you like.

If all else fails, of course, there's always the low-tech solution: Amazon sells "HDMI dummy plugs", dongles that plug into an HDMI port and pretend there's a monitor connected. If you're anything like me, though, that solution won't satisfy you, so I'm here to help if you need help getting some combination of the above working.