Re: Binding Energy

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Mar 08 2004 - 13:23:38 CST

Hello,

Yes this was discussed last month.
quick synopsis:

binding energies include an entropy term not easily determined from
classical methods. Interaction energies can be gained by looking at the
the totalpotential energy of the complex minus the sum of the potential
energy of protein alone.

As Iona pointed out this value ( the difference of two rather large
numbers) may not be relevant given error bars of each calculation.

I proposed that a some MD simulations could get the noise down enough to
gain a reasonable answer.

Brian

On Mon, 8 Mar 2004, Ahmet Bakan wrote:

> Hi All,
>
> As far as I remember that following question was discussed, however I
> cannot find it on the group page.
> Here it is,
> How do you calculate binding energy of two proteins? Does anyone have a
> script calculating all nonbonded interaction energy between two chains
> using CHARMM parameters?
> Thanks in advance,
>
> Ahmet
> ==============ABC==============
> Ahmet Bakan
> Chemistry, Junior
> Koc University
> abakan_at_ku.edu.tr
> MSN ahmetbakan_at_msn.com
> ICQ #86167698
> http://home.ku.edu.tr/~abakan
>
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
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