Re: AMBER: Fwd: positive potential energy and large 1-4 EEL

From: David A. Case <>
Date: Mon, 10 Mar 2008 17:19:51 -0700

On Fri, Mar 07, 2008, Mey Khalili wrote:
> I am trying to make a modified Adenine nucleotide for RNA with amber9. I
> followed the antechamber instructions. The charges came from Gaussian. The
> structure looks like it should and after minimization and 1ns of MD, it
> still looks OK. The problem is that its potential energy is positive.

There is per se no reason why the potential energy should be of any particular
sign. The molecular mechanics zero of energy is an arbitrary one, and is not
the same for different molecules. You should continue to check things
carefully, but a positive energy is not prima facie evidence here.

...good luck...dac

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Received on Wed Mar 12 2008 - 06:07:34 PDT
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