AMBER Archive (2008)

Subject: Re: AMBER: setting perioding box in AMBER

From: David A. Case (
Date: Sun Feb 17 2008 - 20:14:31 CST

On Mon, Feb 18, 2008, Vijay Manickam Achari wrote:
> Is that possible in AMBER to determine the box size and shape to our
> preference? Normally we use SETBOX command in xleap to put periodic
> boundary condition. When we use this command , it put rectangle BOX around
> the residue or molecule. If at all we want to define our won shape such as
> monoclinic, is there any way of doing it?

See the "setbox" comand in tleap. Note that this just sets the box, it does
not try to fill it with water or any other solute. You would have to get the
coordinates yourself.


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