Programming ATMega328p using VP812 programmer (for AVR/Atmel chips) I bootloaded an ATMega328p (the one that uses the basic Arduino bootloader). Then, I used the VP812 for dumping other programs written in C (in Atmel Studio).

The process of erasing, blank test, programming and verification are all working fine and it seems that the program is actually being flashed. However, when I insert the same chip (controller) back in the Arduino Uno board, the controller doesn't function as programmed. Also, I am not able to dump any other example sketches.


Does this mean that the chip is damaged?
Does using the bootloaded chip with VP812 cause such problems?


Also, I used the "Write Fuse" option with the standard fuse configuration (all marks checked) in the VP812 configuration dialog box. Did this setting in any way create the problems I am facing now?
Yes - the settings created this problem. You have erased and disabled (via default fuses) the bootloader. It means that your application will run perfectly fine on an Arduino board, but you will not be able to flash over USB.

If you want to use Arduino USB bootloader again then you have to follow this guide