VMD-L Mailing List

From: gozorows_at_uci.edu
Date: Wed May 23 2007 - 14:00:53 CDT

Thanks to all who replied. I should be able to carry out this calculation
without a problem.

Thank you again,

Gabe Ozorowski

> 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
>