AMBER Archive (2003)

Subject: Re: AMBER: how to calculate vibration frequency?

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 03 2003 - 10:59:41 CST

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_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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