Subject: L-J parameters for Calcium ion

From: <[email-masked]>
Date: Tue, 21 Dec 1993 16:44:49 -0400

Dear netters,

I am trying to do some MD simulations involved Calcium ions, but I cannot
find the parameters (sigma and epsiron) of the LJ potential for the ion.
Could anyone provide me these parameters or give me a hint so that I can
find these data.  Also any comment about the simulation of Ca2+ is very
welcomed.

Thank you and best wishes for the holiday season.

Jian Wang
Department of Chemistry
Dalhousie University
Halifax, N.S.
Canada B3H 4J3
Tel: (902)-494-7021
Fax: (902)-494-1310

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From: [email-masked] (Pieter Stouten)
Date: Tue, 21 Dec 1993 17:30:39 -0500

Hi Jian,

>find these data.
Check out: L.J. Bartolotti, L.G. Pedersen & P.S. Charifson, "Long Range
Nonbonded Attractive Constants for Some Charged Atoms", J. Comp. Chem.,
Vol. 12, No. 9, 1125-1128 (1991).
These parameters work well in simulations (claims based on FEP calculations
of hydration free energies). For calcium it gives C6 = 2.58 kcal A^6/mol
and C12 = 35.8 kcal A^12/mol. The paper gives C6 parameters for other metal
ions (Li, Na,K,Rb, Cs, Be, Mg, Sr, Ba, Al, Sc, Cr, Mn, Fe, Cu, Zn, Ga, Ge,
Se, Ru, Ag, Cd, In, Sn, Eu), too, but not always C12 parameters. However,
the authors present a simple scheme to calculate C12 parameters from the
corresponding C6 parameters.

Hope this helps. Cheers, Pieter.

Pieter Stouten, Senior Research Scientist    ||
Computer Aided Drug Design Group             ||
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From: [email-masked] (Bill Ross )
Date: Tue, 21 Dec 1993 18:08:55 -0800

> corresponding C6 parameters.

A word of warning for those converting the A,B form parameters to r*,eps:

The simple translation formulas one can derive to map A,B to r*,epsilon
set the potential to be the same between atoms of the given type under
both conventions.  BUT, note that owing to the different combining rules 
associated with these two forms of notation, the per-atom potentials derived 
this way result in different distances of the minimum for pairs of atoms 
of _different_ types (the depth of the potential is also different but 
is much less sensitive to the combining rules). Thus it was necessary to 
derive the r* values for the Aqvist monovalent cations to reproduce the 
ion-OH2 potential in the A,B scheme (rather than the ion-ion potential) 
in order to get the correct free energies of solvation in water (Bayly
& Miyamoto, unpublished results).

Insofar as ions are more likely to contact oppositely charged atoms than
each other, it makes more sense to translate the parameters with this in 
mind; partially charged atom types of which all instantiations have charges 
of predictable sign may also be worth considering in this light.

Bill Ross