Re: [AMBER] Preparing a system of 7.4 PH

From: Jason Swails <>
Date: Thu, 18 Sep 2014 07:34:14 -0400

On Thu, 2014-09-18 at 11:12 +0500, wrote:
> Hello
> Is there any way to make a system's PH 7.4 instead of making it
> neutral (7) using xleap? For example my protein has the charge of +17.
> In order to neutralize it, I used the command
> addions abc Cl- 0
> But I want to have 7.4 charge on the system?

You are conflating pH and net charge -- two very different things. The
pH does _not_ say what charge the system should have. It tells you,
along with the microscopic pH values of all of the titratable residues,
what the most likely protonation state will be (or, more accurately, the
probability distribution of the various choices of protonation states).

Most of the time what you want to do is assign protonation states to the
most likely value at this pH (the H++ or PROPKA servers can help in this
regard). In some studies (like if you want to see the coupled behavior
of protonation events with other processes like conformational
transitions), constant pH molecular dynamics is the best tool to use.
Note that CpHMD is an advanced technique and requires a good bit of
study to become familiar with.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Sep 18 2014 - 05:00:02 PDT
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