If you mean rotation of the base around the glycosidic angle, you can use a
dihedral restraint.
This old reference might help
https://doi.org/10.1021/ja075128w
On Fri, Sep 8, 2023, 4:52 PM Jing Qu via AMBER <amber.ambermd.org> wrote:
> Dear all,
>
> I am learning to perform the Umbrella Sampling to get the PMF between two
> states of a DNA strand. And I have trouble determining the reaction
> coordinates. The difference between the two states is that the hydrogen
> bonds they form are not the same. I think the transition is more like
> rotating the base in the plane of the base ring (around the z-axis). I see
> that the tutorial examples on Amber's site use reaction coordinates like
> angles or distances. But I can't think of any angle that would control the
> transition of the structures I have. Anyone have suggestions?
>
> Thanks in advance,
> Jing
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Received on Fri Sep 08 2023 - 14:30:02 PDT
