Subject: Re: L-J parameters for Calcium ion

From: [email-masked] (Pieter Stouten)
Date: Wed, 22 Dec 1993 10:25:12 -0500

On Tue, 21 Dec 1993, Bill Ross <[email-masked]> wrote:

>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 [...]
>
I should have provided all data. Bartolotti et al. give for calcium
r* = 1.74 A, eps = 0.0465 kcal/mol, C6 = 2.58 kcal A^6/mol, C12 = 35.8 kcal
A^12/mol.

Apart from the fact that they reproduce hydration free energy differences
well, the attraction of Bartolotti's C6 parameters (pun not intended) is
that they are not optimized in any sense but derived straight from the
hydrodynamic formulation of time-dependent Kohn-Sham theory (don't ask me
what that means).

Happy Holidays, Pieter.

Pieter Stouten, Senior Research Scientist    ||
Computer Aided Drug Design Group             ||
The Du Pont Merck Pharmaceutical Company     ||    Adventures get spoiled
P.O. Box 80353, Wilmington, DE 19880-0353    ||   by being reduced to data
Phone: +1 (302) 695 3515                     ||             --
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From: Gustavo Mercier <[email-masked]>
Date: Wed, 22 Dec 1993 13:46:41 -0500 (EST)

On Tue, 21 Dec 1993 [email-masked] wrote:

> 
> 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
> 

I don't have the reference with me but Dr. Harel Weinstein and Dr.
Kenzi Hori generated parameters for Calcium to be used with Charmm.
Look for references in the mid to late 80's or early 90's.
Dr. Alan Factor used these parameters in his doctoral dissertation
on Calmodoulin.

Dr. Weinstein is the chairman of Physiology and Biophysics,
Mount Sinai School of Medicine, NY, NY. Unfortunately, I don't
have his e-mail address. Dr. Hori is back in Japan after doing
post - doc work with Dr. Weinstein.

Let me know if you can get in touch with them. I may be able to help.

gus mercier
[email-masked]