Re: AMBER: Normal Mode Analysis

From: David A. Case <>
Date: Wed, 15 Aug 2007 15:56:46 -0700

On Mon, Aug 13, 2007, Kresimir Sikic wrote:
> I have one particular question related to Amber's NMA - I would like to do
> the following: take part of a protein (e.g. one HELIX) in .pdb format load
> it into Amber's NMA (Nmode program) and get the following output:
> a.) stable conformation with a minimum of potential energy (new coordinates
> of all atoms, and total potential energy of new structure)
> b.) potential energy of input structure (structure before energy
> minimization).

The above tasks don't seem to have anything to do with normal mode analysis.
You could prepare the system using LEaP, and minimize it using Sander. The
minimization will show you both the initial potential energy and the final


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Received on Sun Aug 19 2007 - 06:07:15 PDT
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