Hello!
I am using ptraj to get a plot RMSD vs time for
(i) Backbone of residues 1 to 420 and (ii) all nonhydrogen atoms of residues 1 to 420.
For this I have prepared a script file as described in the user manual which are as follows:
(i) rms first mass out BB.rms :1-420.CA,N,C [for back bone]
(ii) rms first mass out BB.rms :1-420 [for all nonhydrogen atoms]
Are the respective script files correct? Is the second one represents the nonhydrogen atoms or all atoms?
With my best regards
Sindrila
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Received on Wed Jul 27 2011 - 07:30:03 PDT
