AMBER Archive (2009)
Subject: Re: [AMBER] Protonated or not
From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Fri Jul 31 2009 - 12:32:50 CDT
The answer to your question is not simple.
When you say 'during the simulation which run at pH 7', you mean the
inhibitor ALONE ?
If so, then yes, it should be protonated at pH 7. Please note that at pH
7, with a pKa of 8.4, there is very small amount of anion, but not fully
However: if you mean a pH=7 simulation with the inhibitor bound to the
target, all bets are off !
The protonation state INSIDE the protein cannot be guessed simply by
looking at the pKa in solution.
s. Bill wrote:
> Dear AMBER
> I am just a little confused about the protonation state of Hydroxamate (inhibitor). Its pKa ranging between 8.4 and 9.1. Does it mean, it should be protonated (in its acidic form) during the simulation which run at pH 7.
> I am so sorry, I got confused from the papers, it called the protonated form (sometimes) hydroxamate (it should be called Hyroxamic).
> Thanks in advance
> AMBER mailing list
Dr. Adrian E. Roitberg
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
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