Hello,
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
purpose).
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
http://www.hloeffler.info/ptraj/image_problem.pdb
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.
Hannes.
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Received on Wed Jul 23 2008 - 06:07:37 PDT
