RE: [PyMOL] problem with amber trajectory

[Warren D. <wa...@de...>]

Dmitry,

VMD may have the ability to shift and recombine the molecule relative to
the periodic boundary in order to avoid this dismembered effect, whereas
currently PyMOL does not.  I believe ptraj can do this for you, though
it has been ages since I have tried using PyMOL with Amber.

Cheers,
Warren

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Warren L. DeLano, Ph.D.                    =20
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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Dmitry Kondrashov
> Sent: Saturday, November 19, 2005 9:57 AM
> To: pym...@li...
> Subject: [PyMOL] problem with amber trajectory
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> Hi,
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> I have a prloblem with viewing AMBER trajectory files,=20
> specifically, the topology appears messed up. When I load the=20
> trajectory into the topology object, the structure shows up=20
> dismembered into eight pieces on the vertices of a cude. I=20
> should note that I can load an AMBER coordinate file into the=20
> same topology with no problem, and that the trajectory=20
> displays just fine in VMD.
> I'm using MacPyMol on Mac OS 10.4.3. No error messages appear=20
> in loading the trajectory, here's the last few lines:
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>   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.
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> I appreciate your help,
> Dmitry
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