Hi George,
I had posted the same problem a while ago. MMPBSA.py script uses sander
to do the energy calculations
when decomposition is requested, and another program, mmpbsa_py_energy,
when no decomposition is requested.
If you use sander in both cases, you will get consistent results.
Dam
>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
>
>
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Received on Mon Jul 09 2012 - 13:30:04 PDT
