Sorry Viktor and Warren, but I don't think your suggestions are
applicable. I have only a single protein molecule in my trajectory,
which I kept centered at the origin, so it never traverses the
periodic boundary. I did strip all but 20 waters from it using ptraj
and created the appropriate topology file for it. That topology and
trajectory, as I mentioned, work just fine in VMD. And the problem
begins with the first frame, so its doesn't seem like bounding box
info is messing it up.
What I thought might be the case is that the format of that ptraj-
generated topology might be a little different that what PyMOL
expected, so I decided to try loading the original (fully-solvated)
topology with the original (fully-solvated) trajectory into PyMOL.
Well, all it did was tie up my computer for ~15 minutes and then
crash PyMOL. The trajectory file is pretty large half a Gig) but it
opens fine in VMD, and doesn't tie up my machine.
I'm sorry to keep harping on the VMD thing - I'd much rather render
the trajectory in PyMOL because of its obvious graphical superiority,
but at present I can't do it. Any ideas?
Thanks,
Dmitry
On Nov 20, 2005, at 9:34 PM, Viktor Hornak wrote:
Dmitry,
is your system a single molecule or is it composed of multiple
molecules (e.g. dimer)? Amber should not 'cut' your molecule into
pieces, imaging can only separate molecules in a dimer, trimer or
such. Also, was your system solvated? Did you strip water before
visualizing in PyMOL? There may be an issue with your trajectory
containing box information which might break a correspondence of
trajectory coordinates and topology. To test this, see if the first
frame of your trajectory looks ok but all others don't. ptraj is a
good program to do various manipulations with your trajectory as
Warren suggested.
Cheers,
-Viktor
Dmitry Kondrashov wrote:
Hi,
I have a prloblem with viewing AMBER trajectory files,
specifically, the topology appears messed up. When I load the
trajectory into the topology object, the structure shows up
dismembered into eight pieces on the vertices of a cude. I should
note that I can load an AMBER coordinate file into the same
topology with no problem, and that the trajectory displays just
fine in VMD.
I'm using MacPyMol on Mac OS 10.4.3. No error messages appear in
loading the trajectory, here's the last few lines:
ObjectMolecule: read set 757 into state 757...
ObjectMolecule: read set 758 into state 758...
CmdLoadTraj: "myo_2_20w.trj" appended into object "myo_20w".
CmdLoadTraj: 758 total states in the object.
I appreciate your help,
Dmitry
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