AMBER: about RMSD per residue

From: <>
Date: Wed, 16 Jul 2008 09:48:05 -0400


   Thanks for several response. However, I guess I
didn't make it clear what RMSD per residue means. There
are several papers using RMSD per residue. I am quite
sure it is not RMSF and I don't know how to use PTRAJ
to calculate.  IF you have access to biophysical
chemistry, please check this paper:

                        Biophysical Chemistry 130
(2007) 65&ndash;75   Figure 1C

    any suggestion about how to calculate it is
welcome. Thanks in advance.



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Received on Sun Jul 20 2008 - 06:07:09 PDT
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