In this work, we analyzed the influence of the charge model on the magnitudes of atomic charges and electrostatic energies for the binding of aromatic drug molecules with DNA. The dependence of the charge and energy on the level of theory (HF, DFT (B3LYP), MP2, semi-empirical methods), basis set (STO-3G, 3-21G, 6-31G, 6-31G*, 6-31G**), method of charge computation (Mulliken, Natural Population Analysis, CHelpG, Merz-Kollman), and force field charge (CHARMM27, AMBER99) has been tracked for typical aromatic drugs of different structure and charge state. Recommendations and restrictions have been formulated for the use of particular approaches in charge/electrostatic energy calculations.