Re: AMBER: work with constant pH on amber8

From: David A. Case <>
Date: Wed, 16 May 2007 11:40:42 -0700

On Wed, May 16, 2007, tri nam Vo wrote:

> I'm working with a protein with 175 aa ( 25 titrable sites) which is stable at pH 4.
> I make MD at pH 4, 6, 8
> But the result showed that the ETOT at pH 4 is higher than at pH 8.

This sort of comparison is not apt. There are on average a different number
of protons bound at the different pH values, so you cannot directly compare
the total energies.

The expected results would include titration curves (showing protons bound
at various sites as a function of pH), and structural information from the
trajectory (showing how, for example, the distribution of conformations varies
as a function of pH.

...good luck...dac

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Received on Sun May 20 2007 - 06:07:11 PDT
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