Hi Anu,
It is quite clear that difference in total energy is coming due to
solvation energies calculated by two different methods (PB and GB) due to
their different calculation scheme. You should go through several reviews
article which discuss the PB and GB formulations. Therefore the difference
in total energy calculated by PB and GB methods is often expected. Both
results are correct, however absolute free energy doesn't matter in your
case since you have no experimental data , what matters is- the relative
energy. I would suggest to concentrate on relative binding energies. In
addition, I think absolute free energy in your case (if still you are
interested in it) will be positive because here you haven't calculated
entropy, therefore anyways it is not meaningful [whenever you calculate
entropy ( according to my experience it will be <-30 kcal) total energy in
your case will be positive for both cases].
regards
Kshatresh
On Mon, Aug 26, 2013 at 11:34 AM, anu chandra <anu80125.gmail.com> wrote:
> Dear Amber users,
>
> I am using 'MMPBSA.py' for calculating the binding free energy of
> protein-ligand interaction. But the calculated binding free energy by GB
> and PB method shows a large difference (please see the results below) and
> I am a bit confused about which method really give significant result.
> Unfortunately, I don’t have any experimental data to compare with.
> *
>
> MMGBSA*
>
> **************************************************************************************************
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> VDWAALS -68.5498 3.3641
> 0.4758
> EEL -9.0344 3.7616
> 0.5320
> EGB 45.6452 3.8693
> 0.5472
> ESURF -7.6578 0.1943
> 0.0275
>
> DELTA G gas -77.5842 4.6776
> 0.6615
> DELTA G solv 37.9874 3.8488
> 0.5443
>
> DELTA TOTAL *-39.5968* 4.1714
> 0.5899
>
>
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> ***************************************************************************************************
>
> *MMPBSA*
>
> ***************************************************************************************************
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> VDWAALS -68.5498 3.3641
> 0.4758
> EEL -9.0344 3.7616
> 0.5320
> EPB 32.4824 3.6040
> 0.5097
> ENPOLAR -50.0504 1.0205
> 0.1443
> EDISPER 88.3701 1.0951
> 0.1549
>
> DELTA G gas -77.5842 4.6776
> 0.6615
> DELTA G solv 70.8021 4.0175
> 0.5682
>
> DELTA TOTAL *-6.7821* 3.9336
> 0.5563
>
>
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> **************************************************************************************************
>
>
> Thanks in advance
>
> regards,
> Anu
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards
*******************************************************************************************************************
Dr. Kshatresh Dutta Dubey
Post Doctoral Fellow
Indian Institute of Technology Kanpur
Kanpur, India
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Received on Mon Aug 26 2013 - 00:00:02 PDT
