Re: [AMBER] Simulating Inifinite DNA molecules

From: Jason Swails <>
Date: Thu, 12 Nov 2015 13:28:34 -0500

On Thu, Nov 12, 2015 at 11:56 AM, Balaji Selvam <> wrote:

> Dear Amber Users,
> I would like to simulated infinite DNA molecule.
> I came across similar posts in archives (
> although its very old post.

​The information here is actually still accurate. Amber does not permit
bonds to cross periodic boundaries, so infinite DNA systems are impossible
in Amber right now.

​They will also be very difficult (if not impossible) to correctly build in
tleap, seeing as Amber has never supported PBC-spanning bonds. I know
other packages allow bonds crossing periodic boundaries, but the only one
I'm sure that does it is GROMACS.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 12 2015 - 10:30:02 PST
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