# Re: [AMBER] MMPBSA.py.MPI - Output discrepancies

From: mish <smncbr.gmail.com>
Date: Tue, 4 Jan 2011 11:52:47 +0100

On Tue, Jan 4, 2011 at 11:41 AM, George Tzotzos <gtzotzos.me.com> wrote:

> Happy New Year to all,
>
> I've been running MMPBSA.py.MPI to determine Delta G for a protein-ligand.
> I've also run the program to determine per residue decomposition of entropy.
>
> The same input files have been used in both cases. The the Delta G results
> obtained from Generalized Born differ by ~ 2kcal/mol
>
> For example,
>
> Differences (Complex - Receptor - Ligand):
>
> DELTA G binding = -46.6213 +/- 3.1112
> 0.1663 (given by per-residue entropy
> decomposition)
>
what do u mean by per residue entropy decomposition ?

> DELTA G binding = -44.2279 +/- 2.7619
> 0.1476 (without per-residue entropy
> decomposition)
>
> The same discrepancy of ~2kcal/mol has been observed using the same ligand
> with two (2) other receptors.
>
> The Poisson Boltzmann calculations with and without per residue
> decomposition gave identical values
>
> Differences (Complex - Receptor - Ligand):
>
> DELTA G binding = -34.0898 +/- 3.1112
> 0.1663
>
> My specific questions are the following:
>
> 1. Is there an explanation for this discrepancy in the case of Generalized
> Born while this discrepancy is not observed in the Poisson Boltzmann
> calculations?
>
> 2. The Delta Gs given by the two methods are different by ~10 kcal/mol.
> That strikes me as being too much of a difference.
>
> 3. Is temperature (say 300K) factored in the ENTROPY calculations?
>
> 4. Can one assume that the enthalpy for the six translational and
> rotational degrees of freedom is 6*(1/2)*RT=1.8 kcal/mol at 300K?
> (are u talking about expected entropy or enthalpy ? )
> Thanks in advance and best regards
>
> George
>
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Received on Tue Jan 04 2011 - 03:00:04 PST
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