AMBER Archive (2007)

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

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 14 2007 - 10:18:47 CDT

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.

...good luck...dac

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