AMBER Archive (2006)

Subject: AMBER: Simulating an "average" DNA sequence

From: S. Jamal Rahi (sjrahi_at_mit.edu)
Date: Fri Jul 21 2006 - 22:20:36 CDT

Hi,

I am interested in simulating a DNA molecule that consists of the
following:
Each base pair of the DNA molecule consists of an overlap of all four
base pairs (AT, TA, GC, CG) but the overlapping basepairs don't interact
with one another and the energy of interaction of each constituent base
pair with the rest of the universe is one fourth of what it would be.

If I create the DNA structure, what parameters do I have to tweak in
Amber for this? How can I prevent Amber from including certain
interactions, how can I turn down interactions with everything else?

Thanks,
S. Jamal Rahi

P.S.: I couldn't find this question in the archive. If it has been asked
and answered, I would appreciate if you could provide me the link!

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