We developed a new method to calculate thermodynamic parameters with the Poisson-Boltzmann equation (PBEQ) and molecular dynamics (MD) calculations. This method treats the solvent effect on the solute conformation as a potential of mean force (PMF), so no explicit water is required in the calculation. The usage of the PBEQ enables the reduction of conformational space to be explored, and we used it to calculate the conformational free energy of alanine dipeptide and hydrogen bond forming-deforming (helix-coil) transition free energy of oligopeptides Ace-Ala(3)-NMe in aqueous solution. We found that (i) the conformational free energy of alanine dipeptide agrees with previous works, (ii) the hydrogen bond forming-deforming transition free energy G(helix) - G(coil) was 1.27 +/- 0.27 kcal/mol, and this deviation was small in comparison with the explicit water calculation, (iii) the solvent effect stabilized the hydrogen bond forming conformation, and (iv) electrostatic dipole moment and accessible surface area of polar atoms have an important role for the hydrogen bond forming-deforming transition free energy.