AMBER Archive (2004)

Subject: Re: AMBER: atomicfluct in ptraj

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Apr 14 2004 - 14:14:47 CDT

Qiang Lu schrieb:
>
> Dear all,
>
> I have a question about the command atomicfluct in ptraj. Does it
> align the structure before the calculation of atomic fluctuation?

No, it doesn't.

> What if the whole protein has a movement or rotation during the
> simulation.

You need to align the snapshots to a reference prior to calculating the
fluctuations (see the "rms" command in the ptraj documentation).

Best regards

Holger 

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Dr. Holger Gohlke

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
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