[AMBER] Exclude H-atom from bfactor calculation

From: Mahendra B Thapa <thapamb.mail.uc.edu>
Date: Tue, 2 Jul 2013 16:02:30 -0400

Dear Amber users,

My 'input file' for cpptraj command contains

trajin test.mdcrd
strip : WAT
reference average_structure.pdb
rmsd reference mass .C,CA,N
atomicfluct out Bfactor_byres.txt .C,CA,N byres bfactor

        I have to exclude the contribution of H-atoms in B factor by
residue. I want to make sure that the contents of above input file serve
this purpose. If I need to modify it, please suggest me.
         I had also tried some minor modifications but this input file gave
me the the closest results to the experimental results than other input
files. Previous postings related to bfactor and rms are very useful to me.

Mahendra Thapa
Physics Department
University of Cincinnati, OH
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Received on Tue Jul 02 2013 - 13:30:01 PDT
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