We present the theoretical evaluations on the two new sets of AMBER force field parameters for the two copper(II) nucleases, Cu(BPA)Cl-2 ( BPA = bis(2-pyridylmethyl) amine) and Cu(IDB) Cl-2 ( IDB = N, N-bis(2-benzimidazolylmethyl) amine) based on the DFT/B3LYP level of theory, incorporating with atomic charges calculated by the RESP method. The new force field parameters have been successfully applied in the testing molecular dynamic simulations for the nuclease-DNA combining systems. The developed force field parameters in this work can be applied in DNA-binding modeling for other artificial copper nucleases with same Cu-N type environments. (c) 2008 Elsevier B. V. All rights reserved.