AMBER Archive (2003)

Subject: Re: Questions about statistics output of mm_pbsa?

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Fri May 23 2003 - 08:22:07 CDT

Hi:
   The ligand is the organic molecule,water molecules are receptors. My
purpose is to find out the interaction energy between ligand and water
molecules. I don't know whether there is an easier way to do it, it
seems to me that mm_pbsa is the only tool I can use.

Sincerely
Lishan
On Thu, 2003-05-22 at 20:32, David A. Case wrote:
> On Thu, May 22, 2003, Lishan Yao wrote:
>
> > I did an energy decomposition for one system composed of one
> > organic molecule and several thousand water moleules.
>
> It's not clear from your question what you defined as the "ligand" and
> what you defined as the "receptor" for this example.
>
> Usually, the waters are stripped away, and "ligand" and "receptor" are
> some small molecule, and a larger molecule. It doesn't have to be done
> this way, but without knowing how you divided things, I can't tell what
> mm_pbsa would have done.
>
> ...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
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>