VMD-L Mailing List

From: Brian Bennion (bennion1_at_llnl.gov)
Date: Wed May 23 2007 - 10:34:57 CDT

Hello

An empirical relationship between carmsd and B factors is given below
<deltarmsd>^2= (3B/8PI^2)^0.5

Please correct me if I am wrong.

At 03:53 PM 5/22/2007, gozorows_at_uci.edu wrote:
>Hello,
>
> I am currently running simulations in NAMD, and would like to calculate
>b-factors (temperature factors) from my .dcd files in order to compare
>them to observed values from x-ray crystallography. I have tried
>searching extensively through the submitted scripts and emails, and
>could not find a suitable answer for how to perform this calculation.
>In the past I used the AMBER software, and it had a built-in b-factor
>command, so I assume such a calculation can be performed reasonably in
>VMD/NAMD. Any suggestions will be welcome.
>
>Thank you,
>
>Gabriel Ozorowski
>Department of Molecular Biology & Biochemistry
>University of California, Irvine
>Steinhaus Hall 540
>Irvine, CA 92697-3900