From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Mon Sep 20 2004 - 17:16:43 CDT
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.
Usually, we keep an eye on this list and provide support for the alchemical
FEP implementation in NAMD.
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
> 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,
> 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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