VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Aug 09 2012 - 15:50:47 CDT

On Thu, Aug 9, 2012 at 10:00 PM, Wang Yi <dexterwy_at_gmail.com> wrote:
> set allatoms [atomselect top all]
> $allatoms get beta
>
> You need to read the online manual for VMD keywords.
> By the way, why extracting B-factors from trajectory? Is there any thing
> during your simulation will change the B-factor?

i suppose the question would work the other way around:
provided you do an MD of a crystal, can you measure
the mobility of atoms around their centers and translate
that into an approximation of the beta factor?

i don't know of anything that would be a direct translation,
but the calculation of RMSF values with "measure rmsf"
might be a starting point.

cheers,
     axel.

>
> ___________________________
>
> Yi (Yves) Wang
> Duke University
>
>
>
>
>
> On 2012-8-9, at 下午3:13, flavio seixas wrote:
>
> Hi all,
>
> Anyone knows a tcl script to extract the B-factors values of protein
> residues (or atoms) from namd trajectory file?
>
> I´ll be thankful for any help.
>
> regards,
>
> flavio
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.