Thanks for such a complete test case!
>From my initial examination it seems that although cpptraj can pick up
these non-canonical pairs, it tends not to due to certain cutoffs -
'origincut' and 'zcut'. 'origincut' is related to the distance between
the base reference origins, and appears to be in a different range
when the base pair is non-canonical. 'zcut' is related to the stagger
and is also has a different range when non-canonical. So you can
adjust these to pick up some of the non WC base pairing, but then end
up picking up other stuff on the margins. You can experiment with them
if you like.
In the meantime, I've clearly got to improve non-canonical base pair
detection in 'nastruct'. I'll open an issue on GitHub and hopefully
get to it over the next few days. Thanks for bringing this to my
attention! Let me know if you end up coming across any more issues in
the meantime.
-Dan
On Wed, Mar 20, 2019 at 2:01 PM Jason Imamoto
<jimamoto.mail.usciences.edu> wrote:
>
> Hello,
> Attached are the files that I used to execute the analysis and the output once it was completed. Note.txt file contains the base-pairs that should form non-canonical base-pairs. There are only two frames in the crd file.
>
> Thank you for your time and help.
>
>
> Jason M. Imamoto
> Doctoral Candidate
> Department of Chemistry and Biochemistry
> GH 302
> University of the Sciences in Philadelphia
> 600 S 43rd St. Philadelphia, PA 19104
>
> Email: jimamoto.mail.usciences.edu
>
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Received on Wed Mar 20 2019 - 12:30:03 PDT
