Shopie,
It might be easy to remove the solvent but you have to take into account
that the final solute structures were calculated using different solvent
media...Try to calculate the solute dipole moment, that might help you to
understand the dE in water respect to octanol (where the solute dipole
moment plays a minor role)...
G
>
>
> Dear amber users,
>
> 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??? The difference
> of
> energie d is weaker in octane than in water. However, if I remove the
> solvent
> molecules in the pdb of the finals conformations and if I compute again
> differences d (after a single stage of minimization), the energy
> difference d
> is weaker in water than in octane. Do you can explain me these
> differences?
> Is there a term of solvatation and where can I find it?
>
> thank you very much for your help
>
> Sophie
>
>
>
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Received on Wed May 02 2007 - 06:07:21 PDT
