Checking an Arduino Mega

Hi,
I have an Arduino Mega 2560 R3.
Currently my computer (Win 7 64) doesn't register it (Tools > Port doesn't show the com port it is connected to)
So I can't program it.

Now, a few days ago I accidentally connected 12V to the 5V pin (not a good idea).
I noticed out of the angle of my eye some smoke? and disconnected the power immediately.

Does anyone know how to test what is wrong.
I tried following:
a. connection to USB -> not recognized

b. connecting Serial to an FDTI board (DTR to Reset) and trying to upload a sketch
this produces following error:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer

c.: the previous sketch which I uploaded still works. (its not a complicated sketch and only uses pins 7,8 and 9 for output and pin 6 for a button) So I assume the ATMEL processor still works.

d.: the On and L LEDs on the board are both on
e.: no visible damage to the board

Any idea what else I could try apart from buying a new board?

Could the boatloader have been damaged???

The DTR signal should go through a capacitor before being connected to the Reset pin. On the Arduino MEGA 2560 schematic it is shown as being 100n (100 nano-Farads).

Thank you for the suggestion. Unfortunately I still get the same error.

Still working on it.
I have some Atmel 328P, so I built a breadboard Arduino and used it as an AVR ISP (http://arduino.cc/en/Tutorial/ArduinoISP)
uploaded a new bootloader the the arduino.

This worked without error messages and now the 'L' LED is flashing constantly.
However the board is still not recognized by windows.

I assume, I have uploaded a new bootloader with the blink sketch included.

Now it would be nice to be able to upload other sketches via the 'Arduino ISP'.
Can anyone point me into the right direction on how to do this?

(Pretty steep learning curve in the last few days, but its kind of fun....)

Here my current version:
Breadboard Arduino (Atmel 328P) with ArduinoISP software loaded
then I set:

Tools > Board >Arduino Mega or Mega2560
Tools > Programmer to Arduino as ISP
Tools > Burn Bootloader

This works fine and now the 'L' LED is flashing

so I load the Blink sketch into the Arduino software and change the delays to be able to see a difference in the flashing frequency (changed line 26 to delay(2000))

Now I upload the file with: File>Upload Using Programmer

It seems to work (avrdude output below), but now the 'L' LED just stays on.

Any suggestions on what I am doing wrong?

avrdude gives me following output (verbose mode)

avrdude: Version 6.0.1, compiled on Apr 3 2014 at 23:12:16
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2009 Joerg Wunsch

System wide configuration file is "C:\Program Files (x86)\Arduino/hardware/tools/avr/etc/avrdude.conf"

Using Port : COM7
Using Programmer : stk500v1
Overriding Baud Rate : 19200
AVR Part : ATmega2560
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PA0
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 0x53
Memory Detail :

Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack


eeprom 65 10 8 0 no 4096 8 0 9000 9000 0x00 0x00
flash 65 10 256 0 yes 262144 256 1024 4500 4500 0x00 0x00
lfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
efuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
lock 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00

Programmer Type : STK500
Description : Atmel STK500 Version 1.x firmware
Hardware Version: 2
Firmware Version: 1.18
Topcard : Unknown
Vtarget : 0.0 V
Varef : 0.0 V
Oscillator : Off
SCK period : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.05s

avrdude: Device signature = 0x1e9801
avrdude: NOTE: "flash" memory has been specified, an erase cycle will be performed
To disable this feature, specify the -D option.
avrdude: erasing chip
avrdude: reading input file "C:\Users\Bjoern\AppData\Local\Temp\build896673534544120819.tmp/Blink.cpp.hex"
avrdude: writing flash (1518 bytes):

Writing | ################################################## | 100% 1.55s

avrdude: 1518 bytes of flash written
avrdude: verifying flash memory against C:\Users\Bjoern\AppData\Local\Temp\build896673534544120819.tmp/Blink.cpp.hex:
avrdude: load data flash data from input file C:\Users\Bjoern\AppData\Local\Temp\build896673534544120819.tmp/Blink.cpp.hex:
avrdude: input file C:\Users\Bjoern\AppData\Local\Temp\build896673534544120819.tmp/Blink.cpp.hex contains 1518 bytes
avrdude: reading on-chip flash data:

Reading | ################################################## | 100% 0.97s

avrdude: verifying ...
avrdude: 1518 bytes of flash verified

avrdude done. Thank you.

Well, it uploaded and verified. Did you disconnect the ISP? If not it might be holding the processor in reset.

Yes, I disconnected the ISP. No difference.

I tried something else:
I installed on the breadboard Arduino the ATMega Chip Detector from Nick Gammon (Gammon Forum : Electronics : Microprocessors : Sketch to detect Atmega chip types)

This software shows which chips are connected to the ISP and also prints (in Hex) the contence of the Bootloader and first 256 bytes of the program memory.

After burning the bootloader I get a 'reasonable output' with some 'random' Hex codes and only FF in the program memory

Then I 'upload' my blink software.

And to my surprise when I check the memory with the chip detector, the bootloader and program memory are filled with FF

So, 'File > Upload Using Programmer' seems to erase everything on the ATMega!!!