From: Troy Bothwell <>
Date: Tue 6 Feb 2001 10:36:20 -0800

I am using ptraj to center a 14-mer DNA oligo in an octahedral box of water
following a 2 ns production run. The output image is no longer an
octahedral (like the initial system formed using leap and the solvateoct iso
commands) , but a parallelagram. I'm not exactly sure what is going on
here. Anyone had similar difficulties. Here is my ptraj input file.

 trajout mdprod2.pdb pdb
 center :1-28 mass origin
 image origin center

Thanks for your comments in advance,

Troy Bothwell
Graduate Student
University of Nebraska - Lincoln
Received on Tue Feb 06 2001 - 10:36:20 PST
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