AMBER Archive (2008)

Subject: AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj?

From: Hannes Loeffler (
Date: Tue Jul 22 2008 - 09:08:36 CDT


I am working on some routines of my own for ptraj. Recently I ported my
code from Amber9 to AmberTools 1.0 but there seems to be a strange
problem involving imaging (visual inspection of my trajectory with VMD
shows the protein "poking out" of the water box, i.e. the protein
appears unsolvated if not imaged properly which I however need for my

I first suspected that I called calculateDistance2 wrongly as there is
this new last parameter 'noimage' but after making sure 'noimage' is set
correctly to 0 I still get the same odd results, i.e. a result that
would correspond to an unimaged trajectory. Just to be sure I tried to
manually image parts of the trajectory with transformImage, see
(minimal) script below.

trajin md030.traj
trajout 30.traj netcdf

image origin center

I uploaded the final snapshot of the trajectory (waters only) to
This is the result with ptraj of AmberTools 1.0, Amber9's version seems
to be ok that is a nice orthorhombic box as expected.

I cannot understand what possibly could be wrong as the relevant imaging
code in calculateDistance2 and transformImage appears to be identical
with respect to the orthorhombic case.


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