Re: AMBER: Simulating an "average" DNA sequence

From: David A. Case <>
Date: Sun, 23 Jul 2006 07:47:15 -0700

On Fri, Jul 21, 2006, S. Jamal Rahi wrote:
> 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?

You will need to do lots of code modifications to implement this, as far as I
can tell. Basically, it sounds like a kind of "locally enchanced sampling"
(LES), but with different chemical entities for each of the copies. Others
may wish to chime in here (can CHARMM or other programs do this?), but to me,
it looks like a programming problem of considerable complexity. You should
expect to become an Amber programming guru to takle something like this.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jul 26 2006 - 06:07:03 PDT
Custom Search