Re: [AMBER] MMPBSA: Default inp warnings

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 17 Sep 2014 15:00:05 -0300

Thank you Jason,

Youíre right in your guess. The energies I reported are:

GENERALIZED BORN (inp=1) -22.3955 kcal/mol. (inp=2) -22.7632 kcal/mol (Complex - Receptor - Ligand)

POISSON BOLTZMANN (inp=1) -18.7747 kcal/mol (inp=2) 0.8206 kcal/mol (Complex - Receptor - Ligand)

Are you saying that the Poisson Boltzmann energies should be the same for inp=1 and inp=2?

Regards

George



On 17Sep, 2014, at 2:57 PM, Jason Swails <jason.swails.gmail.com> wrote:

> On Wed, 2014-09-17 at 14:39 -0300, George Tzotzos wrote:
>> Iím using MMPBSA.py.MPI to calculate binding energies. The script Iím
>> using is:
>>
>> Input file for running PB and GB
>> &general
>>
>> interval=2, endframe=10000, verbose=1,
>> # entropy=1,
>> /
>> &gb
>> igb=1, saltcon=0.100
>> /
>> &pb
>> inp=1, istrng=0.100,
>> /
>>
>> Using inp=1 throws out warning messages indicating that inp=1 is the
>> old default
>
> I think the warnings are actually stating that the defaults for _other_
> parameters in the &pb namelist are applicable to the inp=2 model, and
> that they are being changed to the defaults for the inp=1 model that you
> chose. So this is fine.
>>
>> Running the same calculation with inp=2 and comparing the results the
>> discrepancies for the Poisson Bolzmann binding energies are pretty
>> huge
>
> This has been reported a number of times on this list. If inp=2 is
> giving you physically unrealistic results, inp=1 may be the better model
> to use for your system -- this has been discussed quite a bit on the
> Amber list in the past.
>>
>> GENERALIZED BORN (inp=1) -22.3955 kcal/mol -22.7632 kcal/mol (Complex
>> - Receptor - Ligand)
>>
>> POISSON BOLTZMANN (inp=1) -18.7747 kcal/mol 0.8206 kcal/mol (Complex
>> - Receptor - Ligand)
>
> inp=1 is PB only. The GB nonpolar model is basically only like inp=1 (a
> simple SASA-based method that is purely unfavorable). I'm not quite
> sure what the numbers you posted are supposed to mean. I'm guessing the
> first is inp=1 and the second inp=2? If so, I'm surprised the GB
> energies changed at all, and the PB energies certainly indicate a
> difference in the nonpolar binding free energies. Neither is probably a
> great choice for absolute binding affinities, but hopefully relative
> binding affinities show far less dependence on the nonpolar model you
> choose.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed Sep 17 2014 - 11:30:02 PDT
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