Dear Prof. Marcus & Prof David;
I think there is no image problem as the dry mdcrd file has been generated
by using autoimage command
trajin md1.mdcrd
autoimage
strip :WAT,Cl- out prefix stripped
trajout md1_dry.mdcrd
As per the suggestions of Prof D. Case I think the following should work (I
will try it asap).
trajin md1_dry.mdcrd
reference Full_Mini_dry.rst
rms reference out rms_min.dat .CA
average av.pdb * pdb nobox
Then
trajin md1_dry.mdcrd
reference av.pdb
rms reference out rms_min.dat .CA
atomicfluct out bfactor.dat :1-198.CA byres bfactor
I think the above mentioned script is fine. Please point out if there is
any mistake or improvement or easy way that might act well.
Regards;
SB
On Fri, Nov 28, 2014 at 7:22 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Fri, Nov 28, 2014, Soumendranath Bhakat wrote:
> >
> > 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
>
> Above won't work: you need to use the rms command to align the structure to
> the average structure. See the description of the atomicfluct command in
> the
> Reference Manual.
>
> >
> > 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
>
> This is better, but yet better would be to use the average structure as
> a reference. (It's not clear from your email if you are getting really
> large B-factors from this second script or not.)
>
> ...good luck...dac
>
>
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--
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 - 20:00:02 PST
