This is probably not a bug and can probably not be avoided without changing
your simulation protocol.
PM3 and PM6 are quite different model quantum chemistries and there is no
reason to believe their behavior should be qualitatively identical (it goes
without saying that they will be quantitatively different). I doubt that
this "exotic" behavior with PM6 is due to an error in its implementation.
Such a difference is likely either a natural "error" of the model
(*i.e.*predicted behavior that is not physically accurate) or else an
artifact of
your simulation protocol (*i.e. *some stochastic element of the sampling
protocol has caused the samples to diverge). Can you describe more what
your simulation protocol is?
With *any* semi-empirical quantum method, it is probably a good idea to
validate by comparing to a respectable level of *ab initio* theory. It is
of course up to you and a referee as to what is compared. In this case I
would look at proton affinities, but that is just my opinion.
Regards,
Brian
On Thu, Jun 6, 2013 at 2:11 PM, me, Nancy <bwan0408.gmail.com> wrote:
> I am running a QM/MM simulation for the system that contains a hexose
> molecule, a hydronium molecule and water molecules. The hexose and
> hydronium molecules are in the QM region and water molecules are in the MM
> region. When I run it with PM6, I found there is hydrogen atom exchange
> between that on hydroxyl groups of hexose and on hydronium molecule, but
> when I run the system with PM3, there is no hydrogen atom. I wonder if this
> is a bug in PM6. Is there any way to avoid the hydrogen exchange using PM6?
> Thanks.
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Thu Jun 06 2013 - 12:00:03 PDT
