[AMBER] problems with reimage cmd

From: Chiara Pallara <chiara.pallara.bsc.es>
Date: Wed, 18 Sep 2013 10:11:50 +0200

I have some problems to reimage my trajectory using reimage command from
Amber12 cpptraj. My system contains 2 proteins and one Zn+ ion. I
managed to center the two proteins but not the Zn+ ion.

I run this command:
$AMBERHOME/bin/cpptraj start.pdb < reimage.in
My "reimage.in" file is:
trajin din1.mdcrd.gz
trajin din2.mdcrd.gz
trajout din10ns.mdcrd.gz
center :173-208
image familiar
center :173-209
image familiar
center :1-209
image familiar
  209 is Zn+ ion
1-172 is the first protein
173-208 is the second protein (containing Zn+)

Do you know where is the error?
Do you know how I can solve this problem.
Thanks in advance

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Received on Wed Sep 18 2013 - 01:30:02 PDT
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