AMBER Archive (2009)

Subject: [AMBER] how to calculate correct RMSF?

From: Catein Catherine (
Date: Mon Sep 14 2009 - 06:21:52 CDT

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,



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