Past molecular dynamics (MD) studies of boron nitride nanotubes (BNNTs) have used van der Waals parameters from generic force fields, combined with various values for the partial charges on the boron and nitrogen atoms. This study explores the validity of these parameters by first using quantum chemical packages Car-Parrinello molecular dynamics (CPMD) and Gaussian to compute partial charges for isolated and periodic BNNTs, both with and without water. Then in order to test the accuracy of the molecular mechanics force field using our computed charges, the authors calculate the interaction energy between each water molecule in a hydrated nanotube with the nanotube itself using two methods: first using a quantum chemical calculation, and secondly using the molecular mechanics force field. The authors show that in order to obtain satisfactory agreement in the interaction energies the boron and nitrogen Lennard-Jones parameters must be adjusted from their usual values. Modified Lennard-Jones parameters and partial charges, obtained by fitting, are presented as candidates for future MD simulations of hydrated BNNTs.