[AMBER] how to calculate correct RMSF?

From: Catein Catherine <askamber23.hotmail.com>
Date: Mon, 14 Sep 2009 12:21:52 +0100

Dear Prof. Case,

 

Could you mind to the unit of the results?

 

I use the ptraj as follows:

 

trajin xxx.mdcrd

rms first out rms . CA, P

atomicfluct out xxx.apf .CA, P byres bfactor

 

Did I do anything wrong here? The xxx.apf file that I got has a max value of 1000 for one of the flexible residue, if I follow equation to convert bfactor to RMSF

 

RMSF=(value in xxx.apf * 3) / (8 * pi * pi)

 

I should get the maximum RMSF as large as 38 Angstrom, which is unreasonable, I think. Please kindly suggest what is wrong in this calculation? Many many thanks in advanced.

 

Best regards,

 

Cat
 

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Received on Mon Sep 14 2009 - 13:46:24 PDT
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