Hi,
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:
http://dock.compbio.ucsf.edu/DOCK_6/index.htm
See also
http://en.wikipedia.org/wiki/Molecular_docking
Scott
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Received on Wed Aug 22 2007 - 06:07:10 PDT
