Dear Erik Thanks for your reply,
I have another question. By default, Gromacs considers physiological pH value (7), am I right? Based on experimental data, my project should do under the asidic pH (2). You mentioned to pka. Should I use henderson hasselbalch equation? pH = Pka + log ([A-]/[HA]) for acids pH = Pka + log ([B]/[BH+]) for bases For amino acid Lysine (K) with pka = 10.53 ~ 11 for side chain (for simplicity, I rounded the value), 2 = 11 + log ([B]/[BH+]) ===> [BH+] = (anti log 9) [B] Thus, when I use following command pdb2gmx -f *.pdb -lys gromacs ask me: Which LYSINE type do you want for residue 14 0. Not protonated (charge 0) (LYN) 1. Protonated (charge +1) (LYS) I select 1 (Protonated) Is my rationalization true? --------------------------------------------------------------------------------------------------- and for amino acid Aspartic acid (ASP) with pka = 3.86 ~ 4 for side chain (for simplicity, I rounded the value), 2 = 4 + log ([A-]/[HA]) ===> [HA] = (antilog 2) [A-] Thus, when I use following command pdb2gmx -f *.pdb -asp gromacs ask me: Which ASPARTIC ACID type do you want for residue 18 0. Not protonated (charge -1) (ASP) 1. Protonated (charge 0) (ASH) I select 1 (Protonated) Is my rationalization true? --------------------------------------------------------------------------------------------------- If I am wrong, please guide me. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.