AMBER Archive (2003)

Subject: Re: AMBER: infinitely long DNA & moil-view?

From: bishop (bishop_at_tulane.edu)
Date: Tue Oct 14 2003 - 14:24:52 CDT

Robert,
I recently did some simulations like that.
A very short description of them, and how they compare to an elastic rod
model has been accepted for publication in J. Comp. Phys. It should be
out soon. I can send pre-print.

Note that the B.C.s contrain the twist and extension of the DNA if you
pass bonds through the unit cell.

I did the sims with VMD(viz) and NAMD(computing) and amber parmtop files.

The periodicity of the DNA can be enforced using tleap addbond and
setting the unit cell to initially pass between bp.s.
I created the initial DNA w/ 3DNA from Olson's group at Rutgers.

You must be careful during equilibration b/c changes in volume stretch
the DNA.

In summary it's not worse than any other system and solves some problems
w/ end effects (while introducing others...)

I'll be happy to help in any way.

Cheers,
TOm

Endres, Robert G. wrote:

> Dear Amber users,
>
> I have two questions:
>
> 1) is it possible to do simulations of a truely periodic DNA molecule? Looking
> at the DNA tutorial it seems that the DNA has a only a finite oligomer, solvated in a periodic box.
>
> 2) I tried to obtain the latest version of Moil-view (9.1. ?), but could
> not access the proper web pages or links from AMBER home page.
>
> Any suggestions welcome!
>
> Robert
>
>
>
>
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