AMBER Archive (2008)

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

From: Wang,Ying (wangying_at_ufl.edu)
Date: Tue Jun 10 2008 - 14:12:17 CDT

Thanks a lot!!

On Tue Jun 10 12:45:16 EDT 2008, Thomas Steinbrecher
<steinbrt_at_scripps.edu> wrote:

> 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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--
Wang,Ying

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