AMBER Archive (2008)

Subject: AMBER: linear interaction energy

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Thu Aug 07 2008 - 08:55:18 CDT

Dear Amber users,

I want to try to do Linear Interaction Energy calculations with Amber9. Could anybody give me some
references or links that would be helpful?
Does anybody know the exact refenreces of M.M.H van Lipzig et all (2004) ?

Thanks in advance

Best Regards,
Urszula Uciechowska

MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Thursday, July 31, 2008 4:53 pm
Subject: Re: AMBER: how to get the potential energy of a protein from the system
To: amber_at_scripps.edu

> On Thu, Jul 31, 2008, TaoPaul wrote:
> >
> > I am a freshman in MD. As far as I know the resulting potential
> energy (
> > "EPtot" in out file ) was that of the whole system rather than the protein
> > if ran a MD of protien in explicit water. So I wonder to know how to
> > extract the potential energy of the protein itself. Could anybody
> give some
> > suggestions?
>
> Most modern energy routines (including PME and generalized Born) are not
> "pairwise decomposable": so they cannot be written as just a "protein
> part"
> plus a "solvent part" plus an "interaction part".
>
> There *are* some sorts of analyses where it makes sense to extract the
> coordinates of the protein, and compute just its potential energy. The
> MM-PBSA analysis option in Amber automates this process for you. But
> be aware
> that this involves some additional approximations.
>
> ....dac
>
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