It should be noted that all amino acids are described as polymer residues with implied bonds to the i-1 and i+1 residues. The terminal patches applied with the GENErate command determine how the N-term amine and C-term CO2 are modified wrt. the assumed amide linkage. The default patches create the zwitterion form, which is usually correct in the physiological pH range. If one wishes to study more extreme pH conditions, careful study of the protein topology files, including the 'model' file in the toppar/stream subdir, should allow one to create a new patch based on the standard PROP patch (and the model TP2 residue) that is not protonated.