Re: [PyMOL] problem with amber trajectory]

[Viktor H. <ho...@cs...>]

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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