Re: [AMBER] H++ protonation

From: Ramu Anandakrishnan <>
Date: Mon, 18 Jul 2011 19:30:29 -0400

Hi MP,

Actually, H++ should protonate terminal ser. If you want to contact me directly at and send me a copy of your input structure I can take a look at it.


From: Massimiliano Porrini <>
Sent: Mon Jul 18 14:43:51 EDT 2011
To: AMBER Mailing List <>
Subject: [AMBER] H++ protonation

Dear all, I don't know if this email concerns Amber mailing list, but I think this one is the proper forum where I might ask my question. I am using H++ web site to derive the protonation state of my peptide (not capped at the termini). I have experimental data at pH=2 and I noticed that H++ does not protonate the carboxylate group at the C-terminus (which in my case is a serine residue and the related pK is ca. 4 units as far as I know, therefore the C-terminus should be protonated). I am wondering if H++ does not protonate the C-terminus just because it generates files Amber compatible, which indeed does not have a predefined type for a protonated C-terminus residue. If it is so, I guess it is always up to the user adding a proton at the C-terminus accordingly to the pH value, isn't it? Many thanks in advance. Best regards, MP PS: apologies if this subject has already been discussed elsewhere, but I had a look at the H++ FAQS and I did not find anything. -- Dr. Massimiliano
Porrini Institute for Condensed Matter and Complex Systems School of Physics & Astronomy The University of Edinburgh James Clerk Maxwell Building The King's Buildings Mayfield Road Edinburgh EH9 3JZ E-mail : or maxp.iesl.forth.gr_____________________________________________
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Received on Mon Jul 18 2011 - 17:00:02 PDT
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