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ATX 12v connector?

Yes (I assume you are talking about a Pentium 4.) You have to connect the ATX connector and the 12v connector for the computer to work. AMD CPU's do not require this connector, and as such there is not a place for it on AMD-based motherboards.
 
It is an additional connection for 12 V, which is used for powering the CPU. If you don't connect it, then your CPU will not receive any power, leading to sub-optimal performance.

The idea is to make the motherboard design simpler and more reliable, when working with extremely power-hungry and hot chips.

Intel recommended this change to manufacturers of pentium 4 motherboards, because of the massive demands of the CPU. AMD have not made any recommendations, instead they have just advised the motherboard manufacturers of the minimum performance required. As a result most AMD motherboards, have used only the conventional connector.

However, as AMD chips become more power-hungry, some manufacturers are starting to include this connector because of its benefits.
 
If you don't connect it, then your CPU will not receive any power, leading to sub-optimal performance.

Hmm, if the CPU doesn't receive any power, I think sub-optimal performance would be an understatement!

I have an Epox 4G4A+, and it is configured not to use this plug. Most boards are configured to use this connector however, and this is at the request of Intel to provide a steady 12 volts to the CPU. I am pretty sure the CPU will receive power if the 12 volt plug isn't connected, but will be much less stable than it would be with the extra plug. If your motherboard has the plug snidy, plug it in. If not, then don't worry about it.
 
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