The atomic parameters in consistent charge equilibration (CQEq) method were optimized to reproduce electrostatic potentials around the 20 standard amino acid molecules. The introduction of two atom types for hydrogen improves significantly partial charges on hydrogen atoms. Geometry optimizations of a crambin protein were performed using force fields combined with the CQEq. The CQEq charges were found to be more comparable to the Mulliken charges obtained by the ab initio molecular orbital calculation than the fixed charges used in the AMBER force field. Furthermore, the CQEq charges give more realistic charge redistribution between amino acids in the crambin. (C) 2004 Elsevier B.V. All rights reserved.