AMBER Archive (2009)
Subject: [AMBER] how to calculate correct RMSF?
From: Catein Catherine (askamber23_at_hotmail.com)
Dear Prof. Case,
Could you mind to the unit of the results?
I use the ptraj as follows:
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.