AMBER Archive (2009)

Subject: RE: [AMBER] how to calculate correct RMSF?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Mon Sep 14 2009 - 19:57:20 CDT

Thank you Prof. Case.

 

Cat

 

 

 
> Date: Mon, 14 Sep 2009 08:33:29 -0400
> From: case_at_biomaps.rutgers.edu
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] how to calculate correct RMSF?
>
> On Mon, Sep 14, 2009, Catein Catherine wrote:
> >
> > Could you mind to the unit of the results?
>
> Amber reports lengths (such as a root-mean-square fluctuation) in Ang.
>
> > RMSF=(value in xxx.apf * 3) / (8 * pi * pi)
>
> This is not correct. You should replace "value in xxx.apf" above by its square
> root. But why not just leave out the "bfactor" keyword and see what you get?
>
> ...dac
>
>
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