AMBER Archive (2004)

Subject: Re: AMBER: cell dimensions

From: David A. Case (
Date: Thu Feb 05 2004 - 12:00:41 CST

On Mon, Feb 02, 2004, Dave S Walker wrote:

> I think this is a simple question, yet it has remained elusive:
> For the "setbox centers" command in xleap, what is the syntax when I want
> to manually define the dimensions of the enclosed box?

To manually set the box dimensions, you want the "set" command, not the
"setBox" command. (I know that this is not very intuitive....). For

   set <UNIT> box { 25.0 30.0 35.0 }

Here, <UNIT> is the name of your entire system, and the above example
would create a box with x,y,z dimensions of 25,30 and 35 Angstroms.

(Check the bottom of the coordinate (prmcrd) file that you create to make
sure it did what you want.)

..good luck...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to