We present a method for fitting atomic charges to the electrostatic potential (ESP) of periodic and nonperiodic systems. This method is similar to the method of Camparla et al. [J. Chem. Theory Comput. 2009, 5, 2866]. We compare the Wolf and Ewald long-range electrostatic summation methods in calculating the ESP for periodic systems. We find that the Wolf summation is computationally more efficient than the Ewald summation by about a factor of 5 with comparable accuracy. Our analysis shows that the choice of grid mesh size influences the fitted atomic charges, especially for systems with buried (highly coordinated) atoms. We find that a maximum grid spacing of 0.2-0.3 angstrom is required to obtain reliable atomic charges. The effect of the exclusion radius for point selection is assessed; we find that the common choice of using the van der Waals (vdW) radius as the exclusion radius for each atom may result in large deviations between the ESP generated from the ab initio calculations and that computed from the fitted charges, especially for points closest to the exclusion radii. We find that a larger value of exclusion radius than commonly used, 1.3 times the vdW radius, provides more reliable results. We find that a penalty function approach for fitting charges for buried atoms, with the target charge taken from Bader charge analysis, gives physically reasonable results.