AMBER: Positive EPtot in QM-MM

From: Francesco Pietra <>
Date: Tue, 7 Aug 2007 07:34:35 -0700 (PDT)

With Amber9 I am checking QM-MM/AM1 "solvatebox" with a couple of
stereoisomeric cyclohexyl amines for which I have experimental population
distribution in CHCl3 and MeOH.

With CHCl3 solvent box, QM-MM returns averaged negative values for both AM1ESCF
and EPtot. Also, RMS deviations are modest for EPtot (less than 3 per cent).

With MeOH, averaged AM1ESCF values are negative, while averaged EPtot are
positive in a wide range from initial 40ps (20,000 steps) to 400ps (200,000
steps). Also, RMS deviations for EOtot are larger that values of EPtot.

The structure had already been minimized in vacuum (by MMFF94 FF) and from rst
to pdb it is quite OK at the end of MD. I wonder whether any meaning should be
attached to these numbers. Notice that the equatorial amino group is well
exposed to solvation by MeOH, while in the axial position all experimental data
indicate that solvation is prevented.

Comments welcome.

francesco pietra

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Received on Wed Aug 08 2007 - 06:07:38 PDT
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