Do you mean the base rotates out of the duplex? In that case maybe look at
this article
An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies
https://doi.org/10.1021/ct9001575
On Fri, Sep 8, 2023, 5:15 PM Jing Qu <jqu2.ncsu.edu> wrote:
> Hi,
>
> If you're referring to variations of chi torsion angles then that's not
> what I'm trying to say here. I mean that the bases rotate around the z-axis
> (which is the normal vector to the base plane) with the C1' atom as the
> origin. Or with the other end of the glycosidic bond as the origin. Or
> maybe even rotating the base and the sugar ring together as a whole.
>
> Best,
> Jing
>
> On Fri, Sep 8, 2023 at 4:58 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Fri Sep 08 2023 - 15:30:02 PDT
