the default is that each reported RMSD is a best-fit between the selected
atoms in the 2 structures.
On Fri, Dec 9, 2016 at 8:56 AM, Mike Nemec <mike.nemec.uni-due.de> wrote:
> 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,
>
>
> Mike
>
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Received on Fri Dec 09 2016 - 06:00:06 PST
