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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Received on Fri Jul 24 2009 - 18:09:11 PDT
