AMBER Archive (2009)

Subject: Re: [AMBER] Protonated or not

From: Adrian Roitberg (
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
> Bill
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                            Dr. Adrian E. Roitberg
                              Associate Professor
                             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

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