CHEMMOL (V1.0) is a freeware program for the calculation of molecular masses and chemical analyses of compounds. It was written with the organic chemist in mind.
Thus, apart form (most) of the elements a number of organic functional groups and some protecting groups were added. Likewise, all naturally occuring amino acids were added to the database. CHEMMOL readily parses inputlines like CuSO4.Aq5, H2C=CMe-COOPh, [NEt4].[Cl] and even protected peptides like Ac-Pro-Val-Gly-His-OBn without problems.