Dear Amber Community.
I have been doing some clustering analysis recently and was surprised to see that after ptraj performed the clustering the coordinates of the trajectory have changed. This is important to me because before the clustering was done I had aligned all the frames to 3 atomic centers ('mask1') and then performed the clustering on another part of the molecule ('mask2'). So before the clustering is done these atoms are aligned, after the clustering is done none of the clusters have these atoms aligned.
Is there anyway for this to be prevented?
Thanks in advance, Geoff
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Received on Thu Jul 22 2010 - 19:00:03 PDT
