AMBER Archive (2004)

Subject: Re: AMBER: cell dimensions

From: David A. Case (case_at_scripps.edu)
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
example

   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: case_at_scripps.edu 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 | http://www.scripps.edu/case ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu