Dear Professor,
Thank you very much for the reply. To be clear, my question, whether the
MMPBSA method is reliable in calculating the binding energy for such a
large system.
Harikrishna
I'm not sure what you're asking, but the standard deviation is a measure of
the distribution of values you obtain, not the uncertainty in the average.
Any ensemble will have a variety of data points, but the average may still
be well known. If you want to know how reliable your average or mean is,
you'll need to do analysis on the error in the mean, which it seem you
haven't yet done. Then you can tell how precise your free energy
predictions are.
On Sep 14, 2016 1:30 AM, "hari krishna" <haricoolguy111.gmail.com> wrote:
*> Hi all, *
*> *
*> We have carried microsecond simulations for a protein (800 aa) - RNA
(17 *
*> bp) systems. Various modified RNA molecules have been used to find the *
*> binding specificity/affinity with the same protein. The free energy of *
*> binding was calculated using MM-PBSA method. The entropic contribution
was *
*> calculated using NMODE method. The free energy values (dG) are in the *
*> range of -250 kcal/mol. However, among the various systems used, the *
*> difference in the free energy values(ddG) are in the range of 10 to 30 *
*> kcal/mol. These numbers are more or less to similar to the standard *
*> deviation of the free energy obtained MM-PBSA calculations. Are these *
*> error values obtained from the calculations quantitatively correct? Is
it *
*> safe to report such free energy changes in publications. If not, is
there *
*> any other better way to calculate the absolute free energy other than *
*> approximation methods using AMBER package? *
*> *
*> Harikrishna *
*> _______________________________________________ *
*> AMBER mailing list *
*> AMBER.ambermd.org <
http://AMBER.ambermd.org> *
*>
http://lists.ambermd.org/mailman/listinfo/amber
<
http://lists.ambermd.org/mailman/listinfo/amber> *
*> *
On Wed, Sep 14, 2016 at 11:00 AM, hari krishna <haricoolguy111.gmail.com>
wrote:
> Hi all,
>
> We have carried microsecond simulations for a protein (800 aa) - RNA (17
> bp) systems. Various modified RNA molecules have been used to find the
> binding specificity/affinity with the same protein. The free energy of
> binding was calculated using MM-PBSA method. The entropic contribution was
> calculated using NMODE method. The free energy values (dG) are in the
> range of -250 kcal/mol. However, among the various systems used, the
> difference in the free energy values(ddG) are in the range of 10 to 30
> kcal/mol. These numbers are more or less to similar to the standard
> deviation of the free energy obtained MM-PBSA calculations. Are these
> error values obtained from the calculations quantitatively correct? Is it
> safe to report such free energy changes in publications. If not, is there
> any other better way to calculate the absolute free energy other than
> approximation methods using AMBER package?
>
> Harikrishna
>
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Received on Wed Sep 14 2016 - 11:00:02 PDT
