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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Received on Thu Jun 06 2013 - 11:30:02 PDT
