[AMBER] Problem related to the RMSD

From: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>
Date: Thu, 28 Jul 2011 15:55:30 +0530 (IST)

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 Thu Jul 28 2011 - 03:30:03 PDT
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