Re: AMBER: how to calculate vibration frequency?

From: David A. Case <case.scripps.edu>
Date: Wed, 3 Dec 2003 08:59:41 -0800

On Wed, Dec 03, 2003, A. Hungie wrote:
>
> I am using Amber 6 package. I have 20 ps MD trajectory file stored every 2
> fs of DNA configurations (performed by SANDER).
> I would like to calculate the vibration frequency of nucleobases along the
> trajectory. What module of AMBER6 can be used?

This is what the quasih program does. Source is in amber6/src/nmode.

...good luck...dac 

-- 
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David A. Case                     |  e-mail:      case.scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Wed Jan 14 2004 - 15:53:04 PST
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