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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Received on Fri Nov 28 2014 - 09:30:03 PST
