Re: AMBER: size of solventbox

From: Fabien Cailliez <>
Date: Wed, 23 Feb 2005 12:21:52 +0100

Ca2+ ion Lennard-Jones parameters are available in parm99.dat (atom type
To use them, you have to modify ions94.cmd (see
or do it directly with leap.
Be aware that these parameters are really different from those derived
from Aqvist parameters
(you can find these parameters at :
Anyway, I used the calcium parameters from parm99.dat in my MD and it
seemed to work correctly
(distances with ligands correct, no disruption of the binding sites...).

Good luck,

Germán Sciaini wrote:

> You have to define Ca++ by using of tleap and atom types command. Have
> a look if Ca++ is or not included in the amber default parameters....
> G.

Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail :
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
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Received on Wed Feb 23 2005 - 11:53:02 PST
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