DE0-NANO Board External Clock

So matlab is generating your project and doing a bad job of it. It is instantiating a PLL which, as has been pointed out, is being configured incorrectly.

In the interests of checking your hardware mod, restore the specified clock frequency (in matlab) back to what it was - 50MHz I presume - and see if that runs on your modified hardware. Whilst it may not work exactly as expected it should be sufficient to establish whether you've been successful in modifying your board.

Then you can go about finding a work around for matlab's apparent blunder. You say "I dont use any pll ". Matlab clearly has. I think you need to start there.

Cheers,

Alex