Hello,
You should read the following paper and use it as a tutorial - it's what I
would do: https://pubs.acs.org/doi/10.1021/acs.jctc.2c00291
The Introduction cites about 20 other papers you should also read.
My quick reading tells me that the G-quadruplex is solvated in tleap with
K+ ions, and they find the right locations during careful equilibration.
You don't need to run simulations to understand that without K+, the
G-quadruplex will not be stable, but others may have more insight.
-Christina
On Wed, Jul 2, 2025 at 3:41 PM Debarati DasGupta via AMBER <
amber.ambermd.org> wrote:
> Hi Amber experts,
>
> I was wondering do you have any suggestions/tutorials for simulating RNA-G
> quads? I am trying to run a long scale MD on this PDB 7SXP with and without
> the K+ ion
> I have never simulated G-quads and wondering what is the setup in tleap to
> place the K+ in the center and coordinate it to the 4 G tetrads?
>
> I am wanting to run this in the presence and absence of K+ ion chelated in
> the center just to better understand the impact of the ion for the G quad
> stability.
>
> Any tutorials I can follow for system preparation?
>
> Thanks
> Debarati
>
>
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Received on Thu Jul 03 2025 - 07:00:02 PDT
