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/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 28 2014 - 08:00:03 PST
