Re: AMBER: nucleic acid electrostatic energy

From: David A. Case <>
Date: Sat, 4 Aug 2007 08:28:36 -0700

On Sat, Aug 04, 2007, Tiago Sobreira wrote:
> For Base A and T the EELEC was negative and Base G and C was positive. Any
> one has any idea why this happeed?

Electrostatic energies in molecular mechanics are relative numbers, not
absolute ones. For example, electrostatic interactions are ignored between
atoms bonded to each other, or bonded to a common third atom. This "missing
piece" might be very different for different molecules. So you cannot expect
to draw conclusions from just looking at the average energies of two different
species and noting that one is positive, another negative.


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Received on Sun Aug 05 2007 - 06:08:09 PDT
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