im actually not sure where you got your information from dont mean it in a bad way
Matter:
Matter - Wikipedia, the free encyclopedia
Matter is anything that occupies space and has rest mass (or invariant mass).
Atoms:
Atom - Wikipedia, the free encyclopedia
The atom is a basic unit of matter
Matter is defined as something which occupies space and has mass.

An atom is 99% empty space
Yes, I know the fact that most of an atom is empty space, though it still does take up space and it still does have mass.

If atoms did not possess mass, that would (by definition) mean that nothing in our world took up space and that nothing had mass, thus you would have a total sum of nothing. This would also mean that big and heavy objects like Earth would not have any kind of gravitational effect.

So I'm not really sure where you are getting at, at all.