atmega 2560 is Heating

I'm trying to build a marlin 1.1.9 based 3d printer with ramps 1.4 and arduino mega 2560
i,m using ATX power supply to power the kit including LCD display

my problem is when i connect PS_ON, 5V and +5V(Stand By) from ATX to ramps PS_ON, 5V and VCC respectively without soldering diode D1 on RAMPS board to power up the kit without turning ATX ON as said by reprap, my Atmega 2560 heat too much.
and few seconds later my stepper driver (A4988) for extruder E0 also starts to heat while there was no connection issue.

what are the possible reasons and solution..?

On the ramps is a 3 pin connector. vcc, 5v, ps-on.
Yes D1 needs to be removed (its the diode under the stepper drivers, not the one near the fuses)

You only connect atx standby power to the vcc pin and atx ps on connected to ramps ps-on

The ramps 5v pin is only used if you have something connected to the servo block of connectors, do you have anything plugged in there?

You also plug 12v from the power supply into the ramps power plugs like normal.

NB while in this mode do not also plug in a USB cable, the 5v from the usb will fight with the standby power of the supply and cause issues. (as the two 5v are never exactly both 5v) If you wish to use a usb cable you need to cut the 5v wire in the cable or modify the mega pcb to cut the 5v usb track.

Yes i did that..
But ramps VCC is connected to 5V of arduino mega so connecting +5V SB of atx to ramps VCC means Connecting it to 5V of mega but this pin in mega is build for giving 5V output
so while giving +5V to this pin, at first the mega turns ON but few seconds later it starts to heat and also text on LCD display disappeared.
i also connect the +5V SB from ATX to 5V of mega and a GND from ATX to GND of mega without inserting the RAMPS board, same things happen my mega turns ON but atmega 2560 starts heating
so in my case my mega does not support giving +5V(from any source) to 5V pin of mega
So what should i do?

Just sounds like a half dead mega2560 chip... replace it

But first just check one common fault. Many many people plug their endstops in backwards shorting 5v to gnd via the switch. (instead of connecting signal to gnd)
Make sure this is not the case... if in doubt remove all endstops from the ramps