On Wed, Apr 12, 2017 at 10:06 PM, David Case <david.case.rutgers.edu> wrote:
> On Wed, Apr 12, 2017, James Kress wrote:
>
> > If I have a reference DNA oligomer like:
> >
> > CGCGAATTCGCG
> >
> > And want to do an rmsd against a trajectory of a DNA oiligomer like:
> >
> > GCGCTTAAGCGC
> >
> > Will rmsd reorient the reference (or trajectory) so that the sequences
> > are properly compared, i.e. the AATT sequence in the reference is
> > compared to the TTAA sequence in the trajectory where the A's and T's
> > are compared against A's and T's instead of T's being compared to A's?
>
> In spite of Jason's comments, the short answer is "no". I think you need
> to
> clarify (for yourself) the explicit definition of a "proper comparison".
>
Ah, I misaligned the T's and A's when I was reading and thought you were
trying to compare both sequences in the same order. Indeed, there's no
automated way to do what you want here.
All the best,
Jason
--
Jason M. Swails
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Received on Thu Apr 13 2017 - 06:30:03 PDT
