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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 02 2025 - 13:00:02 PDT
