Re: [AMBER] using thermodynamic integration, how to deal with absolute pka and conformation change

From: Junjian Miao <>
Date: Fri, 18 Mar 2011 11:32:55 +0800

thank you very much for your prompt reply!

if i just want to get the conformation change free energy, such as B --> B', how to do it ? is there a tutorial for it? with respect to

A + B --> AB', can i devise a process like this, A + B --> A + B' --> AB', to compute the overall free energy?


----- Original Message -----
From: "David Case" <>
To: "AMBER Mailing List" <>
Sent: Wednesday, March 16, 2011 9:25 PM
Subject: Re: [AMBER] using thermodynamic integration,how to deal with absolute pka and conformation change

> On Mar 16, 2011, at 8:58 AM, "Junjian Miao" <> wrote:
>> regarding thermodynamic integration, i have a couple of questions, one is can i use it to simulate absolute pka, for example, CH3COOH + H2O -->
>> CH3COO- + H3O+ ?the tutorial A6 demonstrates how to simulate the relative pka, however no comments about absolute one.
> You can't get absolute pKa's from molecular mechanics. Google on something like "DFT absolute pka".
>> another is, for instance, as for reaction A + B --> AB', where the conformation of B changes significantly, in this case, how to simulate the reaction to get the absolute free energy?
> There is no general answer, since it depends on the nature of A and B, and the amount of change. The mailing list is not a good way to get such general questions answered. Try to find papers or reviews that describe problems similar to yours.
> ..dac
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Received on Thu Mar 17 2011 - 21:00:03 PDT
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