AMBER Archive (2004)

Subject: Re: AMBER: factor used in b-factor calculation

From: ML (
Date: Tue Mar 09 2004 - 04:36:57 CST

Dear Fabian,
first, I assume (8/3)*pi*pi is right. Don't know 'bout ptraj homepage
but in the manual on pg.200 it says correctly.

Some literature: correlation of B-factors from MD and x-ray (bzw. NMR)
is Sun Y-C, Yang S-F et al, (1999),J Comput Chem, 20,546-562 or Luo X,
Kato R, Collins JR, 1998, JACS, 120,12410-18 and a book Brooks CL,
Karplus M, Pettitt BM. Proteins: A theoretical perspective of dynamics,
structure, and thermodynamics. New York: John Wiley & Sons; 1990. 259 p.

Hope this helps,


Martin Lepsik
Dept. of Molecular Modeling
Institute of Organic Chemistry & Biochemistry
Czech Academy of Sciences
phone: +420-220 183 540
fax:+420-220 183 292

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