The Browndye2 software lumps all the charges of the residue into one point charge, which may be acceptable for a protein, as in the case of the receptor.pqr file where all the atoms of a particular residue have the same numbering. But for a small ligand, the accuracy can be further improved if we consider each atom as a point charge. This is accomplished by renumbering the atoms of the ligand, each with a different number.