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 : mozz76.gmail.com or maxp.iesl.forth.gr
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Received on Mon Jul 18 2011 - 12:00:03 PDT
