Hi George,
These are two different GB models. While both follow the OBC equation (see
the Onufriev, Bashford, Case paper describing them, cited in the Amber
manual), the alpha, beta, and gamma parameters are different between the two
of them, so you can't expect the results to be the same.
Try using the same GB model and you should get the same results.
Good luck!
Jason
On Tue, Jan 4, 2011 at 12:35 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi Jason,
>
> Many thanks for the comprehensive replies.
>
> With regard to your question if the difference is between the serial and
> parallel implementations of MMPBSA.py the answer is NO. Both runs were made
> with the parallel implementation.
>
> The only difference is that in the per-residue decomposition igb was set to
> 5 (default) whereas in the calculation of total energy igb was set to 2.
>
> Please see the namelists below.
>
> George
> ==========================
>
> Per-residue GB and PB decomposition
> &general
> endframe=50, verbose=1,
> /
> &gb
> igb=5, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
> &decomp
> idecomp=1,
> dec_verbose=1,
> /
> ===========================
>
> Input file for running PB and GB
> &general
> endframe=50, verbose=1,
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
> ============================
> On Jan 4, 2011, at 7:59 PM, Jason Swails wrote:
>
> > Hello,
> >
> > My comments are below.
> >
> > On Tue, Jan 4, 2011 at 3:41 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
> >>
> >
> > Is this the difference between parallel and serial or the difference
> between
> > decomp turned on and decomp turned off? Also, what individual terms
> differ
> > between the two calculations? It could be that the algorithm used to
> > compute the surface area between the two methods is slightly different.
> >
> >
> >>
> >> For example,
> >>
> >> Differences (Complex - Receptor - Ligand):
> >>
> >> DELTA G binding = -46.6213 +/- 3.1112
> >> 0.1663 (given 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
> >>
> >
> > As far as I know, the surface area is non-decomposable for PBSA, so this
> is
> > not really a factor. Hence, you get similar/identical results.
> >
> >
> >>
> >> 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.
> >>
> >
> > This is not unusual, and reflects the method's shortcomings when
> calculating
> > absolute binding free energies. A better comparison to make would be the
> > DELTA Delta G between different receptors with the same ligand or
> different
> > ligands with the same receptor.
> >
> >
> >>
> >> 3. Is temperature (say 300K) factored in the ENTROPY calculations?
> >>
> >
> > Yes. There should be a comment in the output file saying exactly that.
> On
> > the tutorial website, the last line of text in the output file says
> >
> > NOTE: All entropy results have units kcal/mol. (Temperature has already
> been
> > multiplied in as 300. K)
> >
> >
> >> 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?
> >>
> >
> > No. The entropy is calculated from statistical mechanical equations
> using
> > the partition function assuming that the translational, rotational, and
> > vibrational parts of the Hamiltonian are separable. This introduces a
> > mass-dependence of the translational entropy.
> >
> > Note that this email was begun in response to your first message, so my
> > later email will address future questions.
> >
> > Good luck!
> > Jason
> >
> >
> >> Thanks in advance and best regards
> >>
> >> George
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 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. Graduate Student
352-392-4032
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Received on Tue Jan 04 2011 - 14:00:04 PST
