[AMBER] H++ protonation

From: Massimiliano Porrini <M.Porrini.ed.ac.uk>
Date: Mon, 18 Jul 2011 17:34:23 +0100

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 its
pK is ca. 4 units as far as I know, therefore the C-terminus should be

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,

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
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
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Received on Mon Jul 18 2011 - 10:00:02 PDT
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