You need to use AmberTools 12 with at least bugfix 16.
cpptraj is a separate, although similar program to ptraj.
Read the manual to learn more about it.
You should make a command file that uses a sequence
similar to the following:
parm <prmtop file>
trajin <mdcrd file>
autoimage
rmsd <rmsd commands>
Then you can execute: cpptraj -i command.file
Unless you have a complicated solute system, you should
get the correct results.
--Niel
________________________________________
From: Sindrila Dutta banik [sindrila.duttabanik.yahoo.com]
Sent: Sunday, November 04, 2012 10:43 AM
To: AMBER Mailing List
Subject: [AMBER] Problem related to RMSD
How to use "autoimage command in cpptraj"
I modify the script as follows:
center :1-794 mass origin
image origin center
But the result is same. How to rectify this?
Sindrila
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Received on Sun Nov 04 2012 - 10:00:03 PST
