Your post is not clear, but it sounds like the nut is stuck near the top of the valve stem. If true, it indicates that the nut and valve stem are cross threaded. Use two pliers and what ever force is needed to remove the nut. Then just leave the tube without a nut, no harm (even if you stripped the stem threads getting the nut off).

If you pull the stem off of the tube, then replace the tube and use more care to NOT cross thread the nut.