Re: AMBER: How to carry out drug-dna complex simulations

From: Scott Brozell <>
Date: Sun, 19 Aug 2007 11:06:22 -0700


On Tue, 14 Aug 2007, David A. Case wrote:

> On Tue, Aug 14, 2007, Anju Sharma wrote:
> > I want to carry out the simulation so of drug-dna complex. i.e. to carry out
> > simulations by placing the drug molecule at particular site in my dna
> > sequence (intercalating site). i have pdb files of both drug and dna
> > sequence. Now can anyone guide me how to place my drug at the desired
> > location in dna seq using Amber.
> In spite of the "MB" in its acronym, Amber is not a very powerful model
> building program: it generally assumes that an appropriate starting structure
> is available. My suggestion is to find an drug-dna complex in the pdb
> with an intercalating drug similar to yours, then change the drug in the pdb
> structure into your drug. You'll probably have to be somewhat inventive to
> get this done.

Dave's suggestion is a good one.
Another idea is to use a docking program
to predict the binding pose of your drug-dna complex.
Such programs include DOCK:
See also


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Received on Wed Aug 22 2007 - 06:07:10 PDT
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