Re: binding constant

From: Oliver Hucke (
Date: Mon Sep 20 2004 - 15:23:20 CDT

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...

Oliver Hucke, Dr.
Biomolecular Structure Center   Health Sciences Building - K418C
Dept. of Biochemistry           1959 NE Pacific St.
University of Washington        phone: (206) 685 7046
Box 357742                      fax  : (206) 685 7002
Seattle, WA 98195-7742          email:

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