[AMBER] Fitting of rms2d

From: Mike Nemec <mike.nemec.uni-due.de>
Date: Fri, 9 Dec 2016 14:56:23 +0100

Dearl AMBER mailing list,

I want to calculate a 2D RMSD matrix using AmberTools14/Amber14
(1) between all frames of one trajectory and
(2) between all frames of two different trajectories.
I tried to figure out in the Manual and searched also in the Amber
Mailing List, how the structures are fitted/superimposed before the RMSD
calculation takes place. I did not find any hints in the Manual, whether
the structures are first optimally superimposed only on one specific
frame (e.g. the first frame) or if the resulting RMSD matrix corresponds
to a pair-wise fit between all structures for which then the RMSD values
are calculated.

Thank you in advance,


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Received on Fri Dec 09 2016 - 06:00:04 PST
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