Hi Pradipta,
Try to center and image your molecule before you fit it:
trajin je_prodcor_1.mdcrd.gz
center :1-198 mass origin
image origin center
rms first mass out wt1md :1-198
atomicfluct out back.apf.rms .CA byatom bfactor
hope it helps,
bimo
> Hi,
>
> I am using ptraj to calculate B-factor from 3 ns
> MD done with AMBER 7.
> ---------------------------------------
> trajin je_prodcor_1.mdcrd.gz
> rms first out wt1md:1-198.CA
> atomicfluct out back.apf.rms .CA byatom bfactor
> --------------------------------------------
>
> However, the calculated B factor is couple of times
> higher than that of the crystal structure.
> I thought generally B factors from MD is lower than
> that in crystal structure. Is it always true? If not
> what could be source of error in my MD (rmsd from
> the crystal structure for CA atoms is about 1.2 Angs)?
>
> Pradipta
>
> ==============================================
>
> This Mail was Scanned for Virus and found Virus free
>
> ==============================================
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--
+++ Jetzt WLAN-Router für alle DSL-Einsteiger und Wechsler +++
GMX DSL-Powertarife zudem 3 Monate gratis* http://www.gmx.net/dsl
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Jun 22 2004 - 15:36:32 PDT
