Hi George,
When you do the per residue decomposition of the enthalpic part of free
energy, the script calculates teh contribution of each specified residue.
Are u decomposing it over all the residues and reporting sum of all the
residues over here like-
DELTA G binding = -46.6213 +/- 3.1112 0.1663
(given by per-residue entropy decomposition)
so is it the sum over all the residues ??
..mish
On Tue, Jan 4, 2011 at 12:02 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Apologies,
>
> I meant per residue free energy decomposition (see
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm)
>
> Thanks
>
> George
>
>
>
> On Jan 4, 2011, at 11:52 AM, mish wrote:
>
> > 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 - 09:30:02 PST
