AMBER Archive (2008)

Subject: Re: AMBER: how to calculate the interaction energy

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Tue Jun 10 2008 - 11:45:16 CDT

Hi Ying,

what you are describing is the MM-PBSA method. It is implemented into
amber and there's a tutorial to learn how to do it:

http://ambermd.org/tutorials/advanced/tutorial3/index.htm

The problem you mention with explicit/implicit solvation is indeed one of
the main points in these types of calculations and MM-PBSA uses a
continuum solvent approximation to circumvent this (but your simulation
can run in explicit solvent). Please note that there are many other ways
to calculate binding free energies than this (e.g. from SMD pulling,
umbrella sampling, FEP...)

Regards,

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Tue, 10 Jun 2008, Wang,Ying wrote:

> Hi, dear all,
>
> I'm trying to calculate the interaction energy of a small organic molecule
> bind to a big protein. I saw there is a equation in the literature:
> Einter=Ecom-Eprotein-Eligand, in which Einter is the interaction energy, Ecom
> is the energy of the whole system after they bind together, Eprotein and
> Eligand are the energy of the isolated protein and the small molecule.
> My question is, if anybody know the procedure to get the interaction energy?
> My understanding is that I put these two molecules together with a suitable
> distance then let them move to close to each other then I can get the energy
> of every step. and then I delete one of the molecule from the whole system
> and perform the same MD on this molecule then I can get the energy of these
> two molecules individually in every md step then I can minus them from the
> energy of the whole system to get the interaction energy. But I use the
> explicit water, like tip3p water box, so the energy contain the water
> contribution. How can I deal with it? Could anybody tell me how to do that?
> Or I should perform this in vacuum or implicit solvent?
>
> Thanks a lot in advance!
>
> Ying
>
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