On Fri, Jul 7, 2023 at 11:49 AM David A Case via AMBER
<amber.ambermd.org> wrote:
>
> I think Dan is correct about needing to see a structure. Parallel strand
> duplexes may have never been tested, and it's not hard to imagine that they
> could fool an algorithm trying to find "Watson-Crick" base pairs.
The base pair determination algorithm was recently updated (version
6.18.0
https://github.com/Amber-MD/cpptraj/pull/1018), so in theory
non-WC base pairing should also be detected (which can be the case in
e.g. Z-DNA, G-quadruplexes etc). However, the new "better"
determination method is only about 4 months old so there is probably
still room for improvement.
-Dan
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Received on Fri Jul 07 2023 - 11:30:02 PDT
