Re: [AMBER] Help on Normal Mode Analysis

From: Jason Swails <>
Date: Thu, 14 Aug 2014 11:19:10 -0400

On Thu, 2014-08-14 at 22:55 +0800, xy21hb wrote:
> Dear all,
> I wonder how I can set up parameters for a simple and pure normal mode analysis on a protein,
> so no GBSA, entropy stuff needed... by using AMBER 9.

"Setting up parameters" is the same for normal mode calculations as it
is for every other type of simulation with Amber -- you need to create a
prmtop file. Many of the tutorials on
cover how to do that.

> Is there any stepwise tutorial?

Not that I know of. Check the Amber 9 manual -- specifically the
chapter about the "nmode" program. See if there's an option that will
tell nmode to dump the eigenvectors and eigenvalues of the Hessian

I'm pretty sure the "NAB" program/language can do this, so if you can't
get nmode to do what you want, try upgrading to AmberTools 14 (free
download) and look at the chapter describing NAB and how to do normal
mode calculations with it.

The basic recipe is pretty simple though -- minimize (normal modes don't
make much sense unless you are in a local minimum where the potential
well can be more reasonably estimated as a harmonic potential), then
compute and diagonalize the Hessian matrix.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 14 2014 - 08:30:02 PDT
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