Thanks Jason,
The difference is in EGB
The question is which of the two results is more reliable? The calculation with or without the LCPO method?
EGB 15.6232 3.4347 0.1536 (per-residue decomposition)
EGB 17.3176 3.5050 0.1567 (no decomposition)
I know that these energies are relative, but for comparison purposes it'd be good to know.
Best regards
George
On Jul 9, 2012, at 5:50 PM, Jason Swails wrote:
> On Mon, Jul 9, 2012 at 7:18 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> I used MMPBSA.py to calculate deltaG of binding of protein-ligand complex
>> after 10ns MD simulation.
>>
>> The result is shown in the following line
>>
>> DELTA G binding = -35.5263 +/- 2.7449
>> 0.1228
>>
>> I then performed per-residue decomposition on the same trajectory and
>> topology files and got the following result
>>
>> DELTA G binding = -37.4528 +/- 2.6611
>> 0.1190
>>
>> The discrepancy in the Poisson Boltzmann calculation was not significant
>> (see below)
>>
>> DELTA G binding = -29.2195 +/- 3.2998
>> 0.1476
>>
>> DELTA G binding = -28.9779 +/- 3.2726
>> 0.1464
>>
>> I'm using Amber11 and AmberTools 1.5
>>
>> Any suggestions regarding the discrepancy observed in the GB calculation
>> would be most welcome
>>
>
> Check the exact place where the differences occur. The SA part of the GBSA
> (the non-polar solvation) is calculated via a different method. When
> decomp is turned on, the icosa method is used (recursively building
> icosahedra around each atom to estimate the surface area), whereas when
> decomp is turned off, the LCPO method is used.
>
> HTH,
> Jason
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Jul 09 2012 - 11:00:03 PDT
