AMBER Archive (2009)

Subject: Re: [AMBER] DNA + intercalator

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Jul 24 2009 - 18:03:06 CDT


> 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?

If the drug intercalates between bases, I would start with it intercalated
because it will probably not achieve that state in normal simulation
times.

Bill

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