From: Steve Seibold <>
Date: Thu, 6 Mar 2008 13:04:01 -0500

Hi Amber

I am trying to obtain an rms from separate regions of my protein. That
is I want to leave out a center fragment of the protein for my analysis.
I have tried the following and derivations of the following, but have
been unsuccessful.



Trajin file.mdcrd

Reference fileref.pdb

Rms reference out file.txt time 5 :1-200.C,N,O :300-400.C,N,O




Notice I am trying to get rms leaving the peptide sequence of 201-299.


Is this possible with ptraj?





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Received on Sun Mar 09 2008 - 06:07:16 PDT
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