Cationic peptide simulation (ph 2)

The difficulty is building a protonated (COOH) C-terminal group. The solution is simple: use a modified version of the CHARMM parameter and topology files which will build a protonated carboxy terminus. The names of the files you need are

• par_all27_prot_na_with_COOH.inp
• top_all27_prot_na_with_COOH.inp

both of which should be available from within /usr/local/charmm27/