[AMBER] Exporting and Boxing Amber Trajectories by Frame

From: Adam Jion <adamjion.yahoo.com>
Date: Mon, 2 Apr 2012 04:38:48 -0700 (PDT)

I'm using Amber for a non-routine molecular dynamics simulation on the crystallization of glycine zwitterions in a triclinic box.
I would like to export each frame of the trajectory as .pdb file with only the glyzine zwitterions extracted. That is, I will be exporting about 10000 individual .pdb files with each file containing only glycine zwitterions.
Furthermore, each glycine zwitterion should be translated back into the box.
Is this possible with Amber's ptraj command?
I'm not interested in the 'centering of solute'. But I need to force back all my glycine zwitterions back into the triclinic box.
ps. I'm having problems with iwrap=1 function. It does not seem to work with my triclinic box. For some reason, my particles are diffusing outside the box.
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Received on Mon Apr 02 2012 - 05:00:05 PDT
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