Re: binding constant

From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Mon Sep 20 2004 - 17:16:43 CDT

Hi,

A more direct apporach would be to use alchemical transformations performed
with the alchemical FEP code of NAMD. For an example, see:

Can Absolute Free Energies of Association Be Estimated from Molecular
Mechanical Simulations? The Biotin-Streptavidin System Revisited
S. Dixit and C. Chipot, J. Phys. Chem. A, 105 (42), 9795 -9799, 2001.

However, I have to warn you that such calculations are by no means routine
work yet. Their success depends on the well-behavedness of your system, and
most of all, of how much time and care you can dedicate to them.
For a more technical point of view, you may find the alchemical FEP tutorial
informative, although it needs a few updates - again. To make short, the
setup part is now a bit simpler than the document says, and it doesn't
require CHARMM anymore.
http://www.ks.uiuc.edu/Research/namd/tutorial/AlchemicalFEP.pdf

Usually, we keep an eye on this list and provide support for the alchemical
FEP implementation in NAMD.

Regards,
Jerome

Le lundi 20 Septembre 2004 22:23, Oliver Hucke a écrit :
> Hi Bora,
>
> the AMBER MD package contains a module that calculates free energies
> from snapshots of an MD simulation.
> You can calculate the binding energy with this module from the
> simulation of the protein ligand complex assuming that the binding
> process does not introduce significant strain of the ligand and/or the
> protein.
>
> The free energy is obtained as the sum of the molecular mechanics
> energy, the solvation free energy and the entropy. The polar part of the
> solvation free energy is calculated either with the Poisson Boltzmann or
> with the generalized Born method. The entropy part can be estimated with
> normal mode analysis.
>
> So, if you can convert your trajectory to the amber format, have access
> to amber and you can prepare the parameter and the topology files in
> amber format for your system, then you could apply this method.
>
> More information can be found in the AMBER manual...
>
> Best regards,
> Oliver
>
> bora erdemli wrote:
> > Hi all;
> >
> > Is there any way to calculate binding constant of
> > protein and ligand complex during MD simulation?
> >
> > thanks in advance...

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