AMBER Archive (2004)

Subject: Re: AMBER: How does LEaP place Na+ ions?

From: Jiten (jiten_at_postech.ac.kr)
Date: Sun Jan 25 2004 - 19:44:36 CST

addions UNIT Na+ n ( n the number of ions to be added)

Counterions are usually placed at the desired positions. In the case you
need to change the the positions, you can move it using xleap or any other
software.

I hope it helps

Best wishes,

Jiten

----- Original Message -----
From: "tang kwa" <nongtangkwa_at_yahoo.com>
To: "Amber" <amber_at_scripps.edu>
Sent: Thursday, January 22, 2004 7:10 PM
Subject: AMBER: How does LEaP place Na+ ions?

> Dear All,
>
> TO neutralize the system containing DNA and water,
> LEaP module can be used to add Na+ ions. Could anyone
> tell me how Na+ ions are placed, at positions of
> bisector O1P-P-O2P, or iterative electrostatic
> calculations?
> Many thanks inadvance.
>
> Yours,
> Tangkwa
>
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