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The problem of an open string in background $B$-field is discussed. Using the discretized model in details we show that the system is influenced by infinite number of second class constraints. We interpret the allowed Fourier modes as the coordinates of the reduced phase space. This enables us to compute the Dirac brackets more easily. We prove that the coordinates of the string are non-commutative at the boundaries. We argue that in order to find the Dirac bracket or commutator algebra of the physical variables, one should not expand the fields in terms of the solutions of the equations of motion. Instead, one should impose the set of constraints in suitable coordinates.
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