The stability of a series of hydrogen-bonded duplexes was studied using molecular mechanics method with a modified AMBER GAFF force field, in which the original atomic charges were replaced by ones that are more appropriate for non-polar solvents. The free energy change of dimerization was calculated in vacuo and good agreement with experimental data was found. It is also shown that the stability of these duplexes increases linearly with the number of hydrogen bonds, in agreement with experimental data. (c) 2005 Elsevier B.V. All rights reserved.