Thank you for you answer.
I am sorry but I wanted to say that the energy values in explicit water are 100
kcal/mol (and not 10 kcal/mol) weaker than in explicit octane.
After the minimization of the full system (protein + solvent) can I have the
energy value of the only protein and not of the whole system?
Thank you very much
Sophie
Selon "David A. Case" <case.scripps.edu>:
> On Mon, Apr 30, 2007, Sophie Barbe wrote:
> >
>
> > I minimized two conformational states of a protein in explicit water and in
> > explicit octane. I compared the energies differences between the two
> states d
> > (Estate2-Estate1) for the two solvent environment. For this, I noted the
> energy
> > at the end of the output file.
> > NSTEP ENERGY
> > 5000 -3.5409E+03
> >
> > In octane solvent, the energies values are much more weaker than in water
> (1
> > kcal / mol against 10 kcal / mol). Why such a difference???
>
> There is no way of telling from the information you provide. The result
> doesn't sound unreasonable. But just looking at the total energy of a
> solvated system after minimization is not a very useful thing to look at.
> You probably need to look at some free energy simulation (such as umbrella
> sampling, or MM-pbsa) in order to average over the solvent configurations.
>
> I know this is not much direct help, but it sounds like you may be trying to
> get a too-simple answer to a more complex problem.
>
> ....good luck...dac
>
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Sophie Barbe
Chercheur Post-doctoral
LISBP- Groupe de Catalyse et Ingenierie Moleculaire Enzymatiques
UMR INSA-CNRS 5504/ UMR INSA-INRA 792
135, avenue de Rangueil
31077 Toulouse cedex 04
France
Tel: +33 (0) 561 559 963
+33 (0) 561 559 273
Fax: +33 (0) 561 559 400
E-mail: sbarbe.insa-toulouse.fr
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Received on Wed May 02 2007 - 06:07:18 PDT
