Thanks Bill. I did multiple runs of perl version and I realized that the
perl version creates a different PB/GB surface for the first frame in each
run. Is it because of using molsurf?
Another question is the perl version uses atom numbers as the input while
python uses residues numbers. So there are differences because of this?
Yi
On Apr 12, 2011 11:27am, Bill Miller III <brmilleriii.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
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Received on Tue Apr 12 2011 - 11:30:03 PDT
