The differences you are seeing in binding energies are most likely due to
slight differences in the input files for each. Certain default values are
different between the perl and python versions. There is also the
possibility of using molsurf with the perl version, but not with the python
version. Given the exact same input file variables and values, both the perl
and python versions of MM-PBSA will yield the exact same answers for the
binding free energy.
-Bill
On Tue, Apr 12, 2011 at 12:22 PM, <anyiphysics.gmail.com> wrote:
> Dear AMBER users,
>
> I'm using MMPBSA to calculate the binding free energy between a small DNA
> molecule and an anti-DNA antibody. The numbers I got have a 2~3kcal/mol
> difference for the perl and python version when I run PB. When I run GB,
> the difference between perl version and python version is much smaller,
> only about 0.3~0.5kcal/mol. Anyone knows the reason for this difference?
> Which version is better for DNA-protein binding? Thanks a lot.
>
> Yi An
> Graduate student
> Department of Chemistry
> Texas A&M University
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Apr 12 2011 - 09:30:07 PDT
