AMBER Archive (2006)

Subject: Re: AMBER: software to visualize normal modes

From: David A. Case (case_at_scripps.edu)
Date: Thu Jun 08 2006 - 12:46:38 CDT

On Thu, Jun 08, 2006, Ross Walker wrote:

> > Could someone tell me which software can we use to visualize
> > the normal modes generated by Nmode (amber8). Could VMD do that?

> http://www.google.com/custom?hl=en&ie=UTF-8&oe=ISO-8859-1&client=pub-4335923
> 679013434&channel=2673479839&cof=FORID:1%3BGL:1%3BBGC:FFFFFF%3BT:%23000000%3
> BLC:%230000ff%3BVLC:%23663399%3BALC:%230000ff%3BGALT:%23008000%3BGFNT:%23000
> 0ff%3BGIMP:%230000ff%3BDIV:%23336699%3BLBGC:336699%3BAH:center%3B&domains=am
> ber.ch.ic.ac.uk&sitesearch=amber.ch.ic.ac.uk&sa=X&oi=spell&resnum=0&ct=resul
> t&cd=1&q=nmode+visualization&spell=1

Depending on your mail reader, the above may or may not be very helpful, and
in any event doesn't discriminate between helpful and unhelpful replies.

There is a link on the Amber web page (http://amber.scripps.edu) to
"visualizing .... normal mode results". That points to how to do this in VMD,
and in my view is probably the simplest approach.

...dac

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