Converting the B factor you included to an RMSF I get about 38 angstroms, which is probably close to the width of your periodic box. It's likely that your protein isn't centered and imaged to your periodic box.
Marcus Arieno
> On Nov 28, 2014, at 10:38 AM, Soumendranath Bhakat <bhakatsoumendranath.gmail.com> wrote:
>
> Dear Amberists;
>
> I wish to calculate B factor but I am getting huge values something like
> 40539.6099
>
> I think I am missing aligning with a reference structure. Below a script
> please see if it is fine or there is any mistake
>
> trajin md1_dry.mdcrd
> reference Full_Mini.rst
> atomicfluct out bfactor.dat :1-198.CA byres bfactor
>
> or this one
>
> trajin md1_dry.mdcrd
> reference Full_Mini.rst
> rms reference out rms_min.dat .CA
> atomicfluct out bfactor.dat :1-198.CA byres bfactor
>
> Please let me know which one of the script ok or will I need to allign it
> against average PDB instaed of Full_Mini.rst?
>
> previously I used the following script but I am getting wired values such
> as 40539.6099
>
> trajin md1_dry.mdcrd
> reference Full_Mini.rst
> atomicfluct out bfactor.dat :1-198.CA byres bfactor
>
>
> Your help will be highly appreciated.
>
> Best;
> SB
> --
> Thanks & Regards;
> Soumendranath Bhakat
> Researcher
> Molecular Modelling and Drug Design Research Group
> Discipline of Pharmaceutical Sciences
> UKZN, Westville
> Weblink: http://soliman.ukzn.ac.za/Home.aspx
> Past: Department of Pharmaceutical Sciences
> Birla Institute of Technology, Mesra, India
> in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
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Received on Fri Nov 28 2014 - 08:30:02 PST
