Forcefield charges for some newly added atom types need to be computed afresh. Gaussian 09 was used to compute the partial charges for these cases. Minimal molecules containing the atom type were chosen to be chargeless (unless a particular atom-type itself was charged). They were all optimized at HF/6-31G* level of theory, and the ESP fit was obtained. Antechamber 41 was used to check the structural integrity of the fragments and to handle the file format conversion from PDB to a Gaussian input format. Finally, Gaussian output was converted to mol2 format , which contains charges. To bring these charges in line with the charges already present in CHARMM, the charges were scaled by a factor of 0.87, obtained by taking the ratio of ESP charges to CHARMM charges in a benzene molecule. These values were not changed if charges were already available.