Re: [AMBER] Regarding - "Help needed on MMPBSA for a system with different protonation states in free & bound forms"

From: Jason Swails <>
Date: Mon, 18 May 2015 09:06:59 -0400

On Sun, May 17, 2015 at 6:05 AM, Shailesh Pandey <>

> Thank you jason for your suggestion
> If you can suggest me some useful reading books/papers ragarding
> How to account protonation state changes in thermodynamic cycle,
> it would be a great help

​This is the basis behind pKa and constant pH molecular dynamics

I worked on this problem extensively in graduate school, and my
dissertation has an introduction to these methods as well as a list of
sources where you can learn more:


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon May 18 2015 - 06:30:03 PDT
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