Hi Jason,
I did not. I'm using ff99SB and gaff. And to answer also Komath, whom I also thank for his input, I'm using in both cases MMPBSA.MPI
Regards
George
On Jul 9, 2012, at 10:03 PM, Jason Swails wrote:
> Do you use the Glycam force field for any part of the simulation, by any
> chance?
>
> On Mon, Jul 9, 2012 at 1:37 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 09 2012 - 14:00:03 PDT
