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