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
Received on Tue Feb 06 2001 - 10:36:20 PST
