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I have an ATmega2560 R3 with a 16u2 on it.  I am having a heck of a time resetting the 16u2 and was wondering if anyone else had some advice on this.  I have an AVRISPmkII and have tried to program the 16u2 with Arduino-COMBINED-dfu-usbserial-atmega16u2-Mega2560-Rev3.hex, however, this has not yet worked.  The System>Device Manager does not show that the ATmega2560 is being recognized.  When I try the loop-back test, of course it fails since the “Found New Hardware Dialog”pops up and therefore there is no COM port to connect to.  The result of going through installing the drivers results in the “Cannot Install this Hardware” dialog.
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I used the 'non combined' for my 2560 and worked nicely, but I think I don't have the R3
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My website: http://ried.cl

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Problem is I need both the 2560 for the analog inputs and the 16u2 for USB/midi interface to the computer.
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A little success.  I am able to execute the loop-back test at this time.  However, I am still unable to program the ATmega2560 through the Arduino IDE.  Any suggestions?
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I'm not sure if this will help anyone debug this but I tried to use the AVR ISP programmer within the Arduino IDE and received the following:

C:\arduino1\hardware/tools/avr/bin/avrdude -CC:\arduino1\hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega2560 -cstk500v2 -P\\.\COM5 -b115200 -D -Uflash:w:C:\WINDOWS\TEMP\build5740842602492432075.tmp\BlinkTest.cpp.hex:i

avrdude: Version 5.11, compiled on Sep  2 2011 at 19:38:36
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "C:\arduino1\hardware/tools/avr/etc/avrdude.conf"

         Using Port                    : \\.\COM5
         Using Programmer              : stk500v2
         Overriding Baud Rate          : 115200
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: ser_send(): write error: sorry no info avail
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Ok, so I seam to have made a little more progress.  I am able to use the AVRISP MkII to program the ATmega2560 R3 chip now.  However, I can not program the chip with the USB cable within the Arduino IDE.  If anyone has experienced this before and been able to resolve this I am still looking for a little help here.

Thanks
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So, in my continued attempt to get the 16u2 into a state in which I can program the ATmega2560 with the USB cable I ran the following command at the cmd prompt:

avrdude -C avrdude.conf -p m16u2 -F -c avrisp
mkii -P COM8 -U flash:w:\arduino1\hardware\tools\avr\bin\Arduino-usbserial-atmeg
a16u2-Mega2560-Rev3.hex  -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -
U lock:w:0x0F:m -v -v -v -v


=====> Here is an abbreviated response after two hours of just letting it run

avrdude: Version 5.11, compiled on Sep  2 2011 at 19:38:36
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "avrdude.conf"

         Using Port                    : COM8
         Using Programmer              : avrispmkii
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer
         AVR Part                      : ATmega16U2
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PC6
         RESET disposition             : possible i/o
         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    20     4    0 no        512    4    128  9000  9000 0x00 0x00
                             Block Poll               Page      Polled
      Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
      ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
      flash         65     6   128    0 yes     16384  128    128  4500  4500 0x00 0x00
                             Block Poll               Page      Polled
      Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
      ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
      lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                             Block Poll               Page      Polled
      Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
      ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
      hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                             Block Poll               Page      Polled
      Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
      ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
      efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                             Block Poll               Page      Polled
      Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
      ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
      lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
                             Block Poll               Page      Polled
      Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
      ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
      calibration    0     0     0    0 no          1    0      0     0 0 0x00 0x00
                             Block Poll               Page      Polled
      Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
      ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
      signature      0     0     0    0 no          3    0      0     0 0 0x00 0x00

      Programmer Type : STK500V2
      Description     : Atmel AVR ISP mkII
      Programmer Model: Unknown
avrdude: Send: . [1b] . [01] . [00] . [02] . [0e] . [03] . [90] . [85]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer
avrdude: Send: . [1b] . [01] . [00] . [02] . [0e] . [03] . [90] . [85]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer
avrdude: stk500v2_command(): failed miserably to execute command 0x03
avrdude: stk500v2_getparm(): failed to get parameter 0x90
avrdude: Send: . [1b] . [01] . [00] . [02] . [0e] . [03] . [91] . [84]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer
avrdude: stk500v2_command(): failed miserably to execute command 0x03
avrdude: stk500v2_getparm(): failed to get parameter 0x94
         Vtarget         : 25.5 V
         SCK period      : 129.2 us
avrdude: Send: . [1b] . [01] . [00] . [0c] . [0e] . [10] . [c8] d [64] . [19][20] . [00] S [53] . [03] . [ac] S [53] . [00] . [00] 2 [32]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer
avrdude: stk500v2_command(): failed miserably to execute command 0x10
avrdude: initialization failed, rc=-1
avrdude: AVR device initialized and ready to accept instructions
avrdude: Device signature = 0x000000
avrdude: Yikes!  Invalid device signature.
avrdude: Expected signature for ATmega16U2 is 1E 94 89
avrdude: NOTE: FLASH memory has been specified, an erase cycle will be performed

         To disable this feature, specify the -D option.
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer
avrdude: stk500v2_command(): failed miserably to execute command 0x11
avrdude: stk500v2_disable(): failed to leave programming mode

avrdude done.  Thank you.


C:\>

Any help would be appre3ciated...
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