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 - 09:00:03 PDT
