No, not that I know of.
The natural position that you see in the roster page for each of your players is just the result of an algorithm that evaluates all of your players' attributes, but it has no effect during the game. I suspect it has a role in the calculation of the weekly salary, but I'm not sure about that.
As for the accuracy of that algorithm, I can tell you that I've had a player drafted as a PG, and every time he had a pop in an "inside" attribute (like inside shot) he turned into a C, then after another pop in an "outside" attribute (like jump shot) he turned back to PG. Surely that's an extreme case but really, I suggest you not to care too much about natural positions.