I had the same problem. The only solution is to install a routerOS x86 + Free License and run dude.npk on it. RouterOS is a mikrotik proprietary system based on Linux Kernel.
For future reference, Dude runs quite happily in WINE, the wiki has pretty good instructions, and below is specific instructions for doing it on Ubuntu 12.04 headless server:
You should try CloudView NMS http://www.cloudviewnms.com . This is what we use. It runs on all the platforms: Linux, Mac OS, Windows.... WebFig, WinBox and other 3rd party GUI tools are easily integrated. We found it amazingly stable and reliable for large networks and that is what we use in all our installations now.