Dear Jason,
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 and also
investigate the effect of hydration *only at the active site region and
also lid 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 claculate whole
free energy of solvation and mask is not defined for this type of
calculation.
Any suggestion will be appreciated.
On Fri, Nov 25, 2011 at 8:27 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, Nov 25, 2011 at 7:47 AM, M. Reza Ganjalikhany <
> ganjalikhany.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I want to calculate solvation free energy of a solvent accessible loop
> in a
> > protein.
> >
> > Is it possible to set the loop as mask in mmpbsa/mmgbsa?
> >
>
> A mask for what?
>
>
> >
> > Any help will be appreciated.
> >
> > Regards,
> > M.Reza
> > _______________________________________________
> > 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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Nov 25 2011 - 13:00:02 PST
