I would like to calculate the net charge of amino acids at pH 7. Is there any R package available for this calculation? Edit: op wants the charge of a sequence, not single AA
There is nothing to calculate, this is textbook knowledge about amino acids, there are amino acids with charged and uncharged side chains. Just look up the charges in Wikipedia http://en.wikipedia.org/wiki/Amino_acid
Edit: you can simply count the positively and negatively charged AAs in the sequence, the difference is the charge of the sequence.
I think you're looking for either of two things. I disagree with Michael that there is nothing to calculate. On one hand, you could make a sort of lookup table using a named array of the amino acids and their pK values, then at any given pH you could access the value and assess the direction of charge. However you might actually be asking something else. At any given pH, only a fraction of any amino acids exist in a given charged state, so perhaps by "net charge" you're looking for the relatives proportion of charge at that pH? In that case I'm not aware of a package (I haven't looked), but it wouldn't be that hard to write a function for the Henderson-Hasselbalch equation (complete with amino acid pK lookup table), that returns this value for any pH. It would only be a few lines of simple code.