Why protons and neutrons dont weight less then their constituents? A system of gravitational attracted objects weight less than the sum of their individual masses becauses it needs energy to move them apart and overcome the gravitational attraction. Same is true for electromagnetic force, where the attraction between opposite charges must be overcome with additional energy to keep the objects move apart, therefore the system has less energy and less mass.
But why this isnt the case for three quarks bound together to form a proton/neutron?. The color force is (in simple terms) also attractive between the three quarks in a bound system and therefore energy must be applied to move them apart. As a consequence, the bounded system of quarks should have less energy (and less mass) than unbound quarks. Why this isn't the case?
 A: Imagine free quarks being brought together to make a baryon. Your intuition is that, since the end product is bound, (i) the total mass-energy has declined and, though you may not have thought of this implication, (ii) putting the difference back in could break the quarks out. Neither is correct.
Tackling (ii) first, if you try pulling quarks out, your energy is spent on the creation of quark-antiquark pairs, and so what's released is new mesons, not the original valence quarks. This is deeply weird when you first learn of it: it's as if we couldn't create cations, because the attempt to remove an electron from a neutral atom simply released positronium.
The difference comes from gluons carrying their own charge; photons, by contrast, are electrically neutral. So not only do quarks emit gluons, the gluons do too. A baryon's three valence quarks are joined by flux tubes of gluons. These tubes can absorb energy, then turn it into mesons, if you try to pull out the original valence quarks.
A gluon has a color and anticolor charge, and can turn into a quark-antiquark pair. This doesn't just give baryons a meson-making party trick; it also means "sea quarks" populate the forcefields between the valence quarks in a baryon. (Gluons are also believed to clump into glueballs.) So if we turn now to (i), what mass do we reduce by a binding energy's worth to get a baryon's mass? Answer: that of many more than just three particles. Another way to put it is to assign multiple notions of mass to a quark: its "current mass" is what we imagined before the baryon formed, but its being in the baryon means it really has a larger constituent mass.
