Changing a live boot able hdd to a normal one

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http://askubuntu.com – I have a a 1 TB 3.0 Freecom Toghdrive with Ubuntu 12.04 and backtrack 5r2 gnome on dual boot. I was creating a boot able usb in backtrack but instead of selecting the usb drive I accidentally selected the Ubuntu partition(damn noobish). I did not realise my mistake until I tried to boot from the hdd. I tried re-installing grub from the alternate install CD but it did not work. Any Ideas? Thanks in advance (HowTos)