Re: [AMBER] Normal Mode Analysis

From: Dwight McGee <>
Date: Tue, 7 Jun 2011 21:07:45 -0400


*nmode* can be used to perform a normal mode analysis but I would suggest
instead using *nab*. The nab section in the AmberTools 1.5 manual has an
example of how to write such a script. You can also take look at
nab program which is in the mmpbsa_py folder in the AmberTools directory as
an example. Hope that helps.

On Tue, Jun 7, 2011 at 7:08 PM, David Cantu <> wrote:

> Dear Amber users/developers,
> I want to do a normal mode analysis of a small protein using nmode in
> Amber.
> However, I cannot find much documentation about nmode in Amber. Are there
> any documents or useful links?
> Can normal mode analysis of a small protein be done using nmode in Amber?
> Thank you,
> David
> _______________________________________________
> AMBER mailing list

T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
"Problems cannot be solved at the same level of awareness that created
                Albert Einstein
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Received on Tue Jun 07 2011 - 18:30:02 PDT
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