In recent years, mechanical systems such as high speed vehicles and railway trains moving on elastic beam structures have become a very important issue to consider. In this paper, a general approach, which can predict the dynamic behavior of a constrained mechanical system moving on a flexible beam structure, is proposed. Various supporting conditions for the foundation support are considered for the elastic beam structure. The elastic structure is assumed to be a non-uniform and linear Bernoulli-Euler beam with a proportional damping effect. Combined differential-algebraic equation of motion is derived using the multi-body dynamics theory and the finite element method. The proposed equations of motion can be solved numerically using the generalized coordinate partitioning method and predictor-corrector algorithm, which is an implicit multi-step integration method.