AMBER Archive (2001)

Subject: ptraj

From: Troy Bothwell (tbothwe1_at_bigred.unl.edu)
Date: Tue Feb 06 2001 - 12:36:20 CST

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.

 trajin mdprod.xyz
 trajout mdprod2.pdb pdb
 center :1-28 mass origin
 image origin center
 go

Thanks for your comments in advance,

Troy Bothwell
Graduate Student
University of Nebraska - Lincoln