Hello!
Perhaps this cpptraj recipe will work for you analysis:
https://amberhub.chpc.utah.edu/stacking-percentage-protein-ligand-complex/
Hope that helps!
Rodrigo
On Sat, Sep 20, 2025, 9:41 AM Debarati DasGupta via AMBER <amber.ambermd.org>
wrote:
> Hi amber users.
>
> I have a RNA ligand complex where my ligand has 3 aromatic rings and is
> sitting on top of a Gquad ( 4 guanine bases) over a course of 1 microsecond
> the ligand shifts around each of the aromatic rings stack with a different
> G and it wobbles around the top face. Now this is getting challenging to
> compute stacking distance and stacking angles.
>
> Is there someone who has used cpptraj for calculating the distance of
> centroid of rings(ligand) to the nucleobase?
> How does one compute percent stacking over time.
>
> I am trying to understand which ring of the ligand is a dominant
> contributor to stacking interactions.
>
> Also a parallel question there are QM calculations to estimate dipoles of
> heterocycles. Has anyone in this group tried some sort of a calculation to
> assess between a benzene pyridine pyrimidine thaizole etc rings what ring
> system has a stronger dipole moment?
>
> Any ideas would be so greatly appreciated
>
> Debarati
>
> Debarati
> Postdoctoral research fellow
> College of Pharmacy
> University of Michigan, USA
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Received on Sat Sep 20 2025 - 09:00:02 PDT
