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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