AMBER Archive (2009)

Subject: [AMBER] DNA + intercalator

From: Rodrigo Galindo (ros_at_servidor.unam.mx)
Date: Fri Jul 24 2009 - 17:22:35 CDT

Hello to all!

I am studying a novel family of anti-cancer drugs and their interaction with DNA.
We have some experimental evidence that these anti-cancer drugs will intercalate
between the bases of DNA and cause cell death, so, I want to simulate and study this possible interaction
using molecular dynamics.

I successfully used antechamber to create the frcmod file required by
xleap and generate the files to run a simulation with sander (inpcrd and prmtop)
of the anti-cancer drug, but I dont know how to join this simulation to a DNA
section and study their posible interaction. We dont have anyinitial structure
and I know that I can use Sirius to manually dock the drug, but, where to begin?
Outside of the DNA? Starting with the drug already intercalated in the DNA?
Near the PO4- group?

Could you please provide some insights for this particular system? Any
help would be great and thank you very much for your time.

Best regards!

Rodrigo.

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