From: John Stone (
Date: Mon Oct 26 2009 - 10:22:21 CDT

  As you might have guessed, this is not really what MultiSeq was
intended for. You could load the trajectory frames as individual
molecules in VMD and that ought to work.
That said, it seems to me that what you're really trying to do here
to "cluster" your trajectory into a set of representative conformations,
and there are probably tools better suited to this task than tricking
multiseq into doing it. Have a look at this plugin developed by
Luis Gracia and see if it's more what you have in mind:

  John Stone

On Fri, Oct 23, 2009 at 07:07:02PM -0400, stephane acoca wrote:
> Dear all,
> I am trying to load an AMBER trajectory into VMD as separate frames in
> order to subsequently use the MultiSeq plugin to find the minimal set of
> frames that are representative of the trajectory. Is there a way to load a
> trajectory as individual files in the MultiSeq plugin or to evaluate all
> the frames of a trajectory in the plugin? Otherwise, how do I load teh
> trajectory frames individually in VMD so that multiseq views them as
> individual protein structures and does its calculations on them.
> Many thanks,
> Stephane

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