Re: [AMBER] MMPBSA: general question

From: George Tzotzos <>
Date: Tue, 07 Jun 2011 19:07:54 +0200


Your points are well taken.

DeltaGs in my case are in the region of -30kcal/mol which is somehow worrisome.


On Jun 7, 2011, at 7:01 PM, Adrian Roitberg wrote:

> well, for starters, look at the fluctuations in the values for free
> energy for the two runs. the difference between the two runs can ONLY be
> thought of as large or small in regards to the absolute value of free
> energy AND the fluctuations.
> For instance, if the value of DeltaG_1 is -100+-2 and DeltaG_2 is
> -102+-2, then you are talking about a difference of 1 % and the
> distribution of free energies being overlapped between the two
> calculations. It would be hard to imagine the method being better than that.
> If in the other hand the values are DeltaG_1 is -5+-0.2 and DeltaG_2 is
> -7+-0.2, then I would worry.
> While I am standing in my pulpit, let me go back to one of my pet
> peeves: "The systems are properly equilibrated." is not a a correct
> statement. At least you have not written "The systems are fully
> equilibrated."
> The nature of the methods and the systems we study precludes the idea of
> equilibration. We do the best we can, but if we truly had an
> equilibrated system (i.e. where EACH conformation is present according
> to its own Boltzmann weight), then we would not have to do mmpbsa or
> anything else. We would already have the answer to any question we wanted.
> I am not sure yet what the proper term should be, but we should maybe
> use 'The systems are sampled in the same way.' or something like that.
> Adrian
> On 6/7/11 6:51 PM, George Tzotzos wrote:
>> Hi everybody,
>> Having run to independent 10ns production runs on the same protein/ligand complex, I observed a difference in Delta G binding of ~ 2kcal/mol. The systems are properly equilibrated.
>> The above difference strikes me as too large. Is this something to be expected?
>> Regards
>> George
>> _______________________________________________
>> AMBER mailing list
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> on Sabbatical in Barcelona until August 2011.
> Email
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Received on Tue Jun 07 2011 - 10:30:04 PDT
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