AMBER Archive (2007)

Subject: AMBER: AMBER MINIMIZATION

From: Sophie Barbe (sbarbe_at_insa-toulouse.fr)
Date: Mon Apr 30 2007 - 08:55:53 CDT

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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