Rade, your question is a little beyond my knowledge. I believe that quarks are subject to all the fundamental forces, including gravity which means that they have mass. I don't know enough about quarks to know if calculating the center of mass of three quarks is a valid thing to do.
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The "effect" would be related the gravitational force. When using Newton's Law of Universal Gravitation F = G\frac{m_1 m_2}{r_{12}^2} to calculate the force between two objects you calculate the distance between the two objects r_{12} as the distance between the center of masses of the two...