Would you like to give your suggestions/hints about the methylated lysine, in particular, the angle parameter of CE (CT2) - NZ - C (Methyl, CT3?)? Thanks you in advance.
i don't think a protonated secondary amine has been studied. do a quick QM calculation on protonated dimethylamine and assign the needed parameter based on the optimized structure. be sure to check that the angle parameters you determine yield the QM angle in the charmm optimized structure.
does any one have topology and parameter file for deprotonated form of proline amino acid. whatever i am getting from www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm
is for zwiterionic form of proline residue.
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.