What about decomposition analysis with MMPBSA?
However, note that the free energy of hydration only at the active site
region of the enzyme is poorly defined. Do you want the free energy as if
the rest of the protein simply didn't exist? Or do you still want the
solvent accessibility (and overall topology) of the active site to be the
same as it is in the entire enzyme, but only calculate the solvation free
energy terms of your active site residues?
What do you want to do with the internal potential terms (bond, angle,
dihedral, etc.): don't count any of them? only count the ones in the active
site? what about the ones that bridge active site and non-active site atoms?
I don't think that you described what you wanted in enough detail. Exactly
what you are trying to calculate (which stems from what you're trying to
learn) will dictate the steps you need to take.
HTH,
Jason
On Sun, Nov 27, 2011 at 11:29 PM, M. Reza Ganjalikhany <
ganjalikhany.gmail.com> wrote:
> Dear Amber users,
>
> I want to investigate the effect of surface hydration on the active site
> region of an enzyme at different temperatures.
> I have already calculated free energy of hydration and also stability of
> enzyme by MMPB/GB-SA.
>
> I have a big challenge to calculate free energy of hydration *only at the
> active site region of my enzyme .*
> (The active site is covered by a solvent accessible lid).
>
> So my question is:
> How to calculate free energy of solvation for that mentioned part of a
> protein?
>
> I couldn't find any solution for my problem since MMPBSA claculates whole
> free energy of solvation
> and mask is not defined for this type of calculation.
>
> Any suggestion will be appreciated.
>
> Regards,
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Nov 27 2011 - 21:00:02 PST
