David,
reference
111
123456789012
CGCGAATTCGCG
DNA
111
123456789012
GCGCTTAAGCGC
Using the command:
rms reference :3-10,15-22&!.H= out rms.dat
where we want to use reference residues 10-3, 22-15 to compare with DNA
residues 3-10,15-22
>From your comments, it would appear that this cannot be done.
Does that make sense?
Jim
-----Original Message-----
From: David Case [mailto:david.case.rutgers.edu]
Sent: Wednesday, April 12, 2017 10:06 PM
To: jimkress_58.kressworks.org; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] reorientation in rmsd
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".
Try starting with just two nucleotides, e.g. the TpA and ApT in the very
center. (These have different conformational preferences.) You could
compare the sugar-phosphate backbones (by stripping out the bases); I can't
think of any good way to compare the base positions, even with manual
manipulation of the coordinates. (However, it's late at night here, so
maybe I'm missing something.) If you figure out what you want, the next
step is to arrange the coordinates so that each atom in the reference
conformation matches the corresponding atom in the trajectory conformation.
....dac
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Received on Wed Apr 12 2017 - 20:00:02 PDT
