External power supply and use of USB

I use an external 5V / 3A power supply due to the large number of different modules that are connected to the Arduino. For example, the Arduino itself would fry a 1.2A LDO, so I use an external power supply.
The problem occurs if I connect a USB that activates the LDO and that burns immediately. Is there a way to protect the Arduino LDO? Diode? What?

Show us a good schematic of your circuit.
Show us a good image of your ‘actual’ wiring.
Give links to components.

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Probably the most important question what Arduino are we talking about? Follow LarryD's recommendation and include links to technical information on all the different modules. A frizzy thing does not count as a schematic. We need to see all the power and ground connections which must be included in the schematic. Show your power calculations so we know the 3A is enough. On my Arduinos unplugging the USB causes the LDO to operate and supply current not the other way around as you state.