Unless I've missed a change, RMS can only be performed between identical
molecules in Amber. If you wanted to compare the overlapping parts in
Amber, you could try stripping the nonoverlapping atoms from each
trajectory and coming up with a prmtop to represent it, but it would be
a painful process repeated in each case. Best thing would be to write
your own RMS code if you can't find any to do it.
Bill
On 4/12/17 10:32 AM, 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?
>
> Thanks.
>
> Jim
>
>
>
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Received on Wed Apr 12 2017 - 11:30:02 PDT
