The restrained electrostatic potential (RESP) fitting method with a harmonic restraint toward target values is applied to determination of atomic charges on polypeptides on the basis of the fragment molecular orbital method. The present RESP charges are determined to be confined around the targeted AMBER 94 charges with high-fitting quality, including structural specificity; an optimal value of restraint weight makes the fitted charges reliable and stable. We employ the optimally-weighted RESP charges for an improvement of force fields in molecular dynamics simulation and show that the charges keep good reproducibility of the electrostatic properties during the simulation. (C) 2008 Elsevier B.V. All rights reserved.