[AMBER] What is the unit for RMSF result?

From: Ashutosh Shandilya <izerokelvin.gmail.com>
Date: Fri, 25 Feb 2011 10:09:30 +0530

On 22 February 2011 12:07, Catein Catherine <askamber23.hotmail.com> wrote:

>
> Dear Sir/Madam,
>
> What is the unit of the RMSF values obtained with the following command?
> Unit of RMSF and Bfactor is essentially the same as Angstrom



> "atomicfluct out xxx.bfactor byres bfactor"
>
Using this formula you are calculating bfactor which is Bfactor =
8/3(2r2) where r is the root mean square fluctuation.


>
> "atomicfluct out xxx.nobfactor .CA,C1',N10 byres"
>
whereas using this command you are calculating root mean square
fluctuation.(RMSF). So when you multiply the output of this file by 8/3(2)
you will get precisely the same value.

>
> The first one ranged from 550 to 5
>
> The second one ranged from 4 to 0.4
>
>> atomicfluct out sc_bfac.dat byres @CA bfactor
>
> atomicfluct out sc_bfac.dat @CA byres
>
> *atomicfluct out sc_bfac.dat @CA byres bfactor*
>
> If you use the highlighted script you will get the same result as bfactor
aka (first script result).

> Which one should be used for publication?
>
You can use any one of them as one is RMSF and other is Bfactor.

>
> Do we need to do the rms first out xxx.rms @CA,C1',N10 before doing RMSF
> calculation?
>
> Thanks a lot.
>
> Best regards,
>
> Catherine



> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 24 2011 - 21:00:02 PST
Custom Search