VMD-L Mailing List

From: gozorows_at_uci.edu
Date: Tue May 22 2007 - 17:53:27 CDT

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