AMBER Archive (2006)

Subject: Re: AMBER: a challenge: a periodic box that cuts through a monomer

From: David A. Case (case_at_scripps.edu)
Date: Tue Mar 21 2006 - 00:29:33 CST

On Mon, Mar 20, 2006, Kenley Barrett wrote:
>
> A member of my research group used AMBER to simulate an
> infinite helix of DNA. Basically, he read the repeat unit of DNA into XLeap,
> created a solvent periodic box, and then manually changed the size of the
> periodic box in the .inpcrd file....

I'm not sure that I understand how this could have worked. Amber assumes
that only nonbonded interactions cross a boundary between two periodic
images. So, I'm not sure how the covalent bonds that connect the DNA
into an infinite helix would be created.

Since doing this sort of thing was never part of the design goal of the
program, I pretty sure some serious thinking and coding changes will be
required to make this work.

[I *think* I've been told that CHARMM can work with such systems, but others
would have to say for sure.]

...dac

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