Although discussion on this topic has died off, I'd like to make a small contribution --- for what it's worth --- after a closer look of my input files (see below).
Question. Is it possible that the discrepancy observed is due to the use of different solvation models (igb=2 cf. igb=5)?
Regards
George
================================================
Input file for running PB and GB
&general
interval=2, endframe=1000, verbose=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
Differences (Complex - Receptor - Ligand):
DELTA G binding = -34.6360 +/- 2.4882 0.1574
Per-residue GB and PB decomposition
&general
interval=2, endframe=1000, verbose=1,
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=1,
dec_verbose=1,
/
Differences (Complex - Receptor - Ligand):
DELTA G binding = -37.0737 +/- 2.3787 0.1064
On Jul 9, 2012, at 10:24 PM, Damodaran, Komath wrote:
> 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 Fri Jul 13 2012 - 12:00:03 PDT
