AMBER Archive (2006)

Subject: Re: AMBER: Amber 8.0 MM_PBSA Stability : question about methodology

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 24 2006 - 14:36:30 CDT

On Mon, Jul 17, 2006, Guillaume Bollot wrote:

> I have a macromolecule which containt 32 LYS and 32 HIS residues (total 64
> residues). I want to know the free energy (absolute free energy) when I
> change manually the protonation state.

To compare free energies of different protonation states, you need to have a
balanced chemical equation. That is, the "extra" protons need to come from
somewhere (usually a hypothetical bath at some pH). Check the "constant pH"
section of the manual (and the references cited there) for some ideas about
this.

> dynamic in gas phase for 5 protonation states

If you really want the gas phase free energies (e.g. for mass spec analysis?),
it will probably require some work, since Amber is really designed for
condensed phase simulations.

...good luck...dac

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