Ca2+ ion Lennard-Jones parameters are available in parm99.dat (atom type
C0).
To use them, you have to modify ions94.cmd (see
http://amber.scripps.edu/Questions/mail/252.html)
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 :
http://amber.scripps.edu/Questions/vdw.html).
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,
Fabien
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 : cailliez.ibpc.fr
IBPC 13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________
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Received on Wed Feb 23 2005 - 11:53:02 PST
