AMBER Archive (2008)

Subject: RE: AMBER: how to extract energy

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat May 24 2008 - 02:24:13 CDT

Hi:
That is a topic of great interest, for example when comparing docked ligands.Quite often, the situation of explicit environment (solvent and other membrane components, remembering that membrane proteins represent about 30% of genetically encoded proteins and about 60% of targets in pharmaceutically oriented studies).

May I ask if the limitation mentioned below for explicit solvent is from theory or is it amenable by further developing the code?

To this regard I would be much interested in opinions about Aqvist's "MD ...free energy perturbation", recently updated: M Nervall, P Hanspers, J Carlsson, L Boukharta, J Aqvist "Predicting binding modes from free energy calculations" J Med Che 2008, 51, 2657-2667. Does it represent a solution of the above "explicit solvent issue"? I know that the proteins in this study are not transmembrane proteins, though the "free energy perturbation" methodology was applied before to transmembrane proteins.

Thanks
francesco pietra

--- On Fri, 5/23/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> From: Ross Walker <ross_at_rosswalker.co.uk>
> Subject: RE: AMBER: how to extract energy
> To: amber_at_scripps.edu
> Date: Friday, May 23, 2008, 8:07 PM
> Hi Wang,
>
> Are you running this simulation in explicit solvent? If so
> then the PME
> routines etc are not strictly pairwise decomposable so you
> can't actually
> evaluate the energy of a single molecule. You can, however,
> obtain the
> internal energy for a molecule (bonds, angles, dihedrals
> etc). If you are
> running implicit solvent GB then you can do a pairwise
> decomposition to find
> an individual molecules contribution to the total energy.
>
> See idecomp on page 26 of the AMBER 10 manual.
>
> Good luck,
> Ross
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf
> > Of WANG,YING
> > Sent: Friday, May 23, 2008 6:08 PM
> > To: amber_at_scripps.edu
> > Subject: AMBER: how to extract energy
> >
> > Hi, Dear ambers,
> >
> > My system contain some molecules. The mdout give me
> the total
> > energy of the whole system. if I want to know the
> energy of one of
> > the molecules but not the total energy of the whole
> system, how
> > can I do?
> >
> > If you know how to do could you tell me? Thanks a
> lot!!
> >
> >
> > Ying
> >
> >
> >
> >
> >
> >
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