Dear hari krishna:
you can find recent analysis of approximations
in continuum solvent binding studies in this review
paper:
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
By: Genheden, Samuel; Ryde, Ulf
EXPERT OPINION ON DRUG DISCOVERY Volume: 10 Issue: 5 Pages: 449-461
Published: MAY 2015
Protein/RNA complexes can be even more difficult even for
basic simulations.
Can We Execute Stable Microsecond-Scale Atomistic Simulations of
Protein-RNA Complexes?
By: Krepl, M.; Havrila, M.; Stadlbauer, P.; et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 11 Issue: 3
Pages: 1220-1243 Published: MAR 2015
all the best Jiri
-------------------------------------------------------
Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer.ncbr.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/
http://www.ibp.cz/en/departments/structure-and-dynamics-of-nucleic-acids/
-----------------------------------------------------------
On Wed, 14 Sep 2016, hari krishna wrote:
> Date: Wed, 14 Sep 2016 23:24:13 +0530
> From: hari krishna <haricoolguy111.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations
>
> 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
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 14 2016 - 11:30:03 PDT
