Re: AMBER: GB Energy Spreads for MD Structures

From: David A. Case <>
Date: Mon, 7 May 2007 14:13:41 -0700

On Mon, May 07, 2007, wrote:
> This might seem to be a silly question, but I'm perturbed as to why
> there is a huge energy spread in the energies I obtain from APBS, much
> like those in figure 1 of this paper (Tsui V., Case D.A., "Molecular
> Dynamics Simulations of Nucleic Acids with a Generalized Born
> Solvation Model", J. Am. Chem. Soc., 2000, 122, 2489). For a
> particular RNA/DNA, MD appears to generate snapshots with
> electrostatic energies (calculated using GB or Poisson Boltzmann) with
> variation of several hundred kT (~300-500).

This doesn't directly address your question, but might be a useful starting


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Received on Wed May 09 2007 - 06:07:19 PDT
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