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

From: David Case <>
Date: Wed, 16 Mar 2011 09:25:26 -0400

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.


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Received on Wed Mar 16 2011 - 06:30:03 PDT
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