Re: [AMBER] protonation of protein-ligand complex

From: Jason Swails <>
Date: Thu, 14 Nov 2013 16:33:58 -0500

On Thu, Nov 14, 2013 at 3:14 PM, Thomas Evangelidis <>wrote:

> Hi,
> calckpka read the output of constant pH MD, therefore is not useful in my
> case. Is there any other third party tool I could use to find the
> protonation of the binding pocket at a given pH value?

You have already used 2 tools. One told you that the pKas and pH are too
similar to reasonably choose a single protonation state. The other told
you they're both deprotonated (as I would expect of almost any glutamate at
pH 7.6), but you were not convinced. Both tools have been calibrated
against experimental measurements and have been shown to reproduce
relatively small (and sometimes even modest) pKa shifts.

The contradictory results indicate that there is no quick-n-dirty tool that
can give you the 'correct' protonation states at your desired pH just by
looking at your initial structure (if, indeed, a 'correct' protonation
state exists at all).

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 14 2013 - 14:00:03 PST
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