Re: AMBER: atomicfluct in ptraj

From: Holger Gohlke <gohlke.bioinformatik.uni-frankfurt.de>
Date: Wed, 14 Apr 2004 21:14:47 +0200

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 

-- 
!!!      Please note new telephone number      !!!
++++++++++++++++++++++++++++++++++++++++++++++++++
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.bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Apr 14 2004 - 20:53:00 PDT
Custom Search