[AMBER] Force field parameters for Magnesium and Calcium in Amber

From: Nadine Schwierz-Neumann <nadine.schwierz.biophys.mpg.de>
Date: Fri, 20 Oct 2017 12:35:06 +0200

Dear all,

I am developing new force field parameters for metal cations with the
TIP3P water model.
Now, I want to compare with force fields from the literature and even
more importantly with the database of Amber.
I have carefully checked the parameters that are in the parm99 database.
All parameters should be the ones adapted from the paper by Aqvist (JPC
1990,94,8021, Table I and II).
In the original paper by Aqvist the force field parameters are given in
terms of A and B.
These can be converted to R_min (in units Angstrom) and epsilon (in
units kcal) via:

R_min=((2*762,89*A/(24,39*B))^(1/6) -1,768)


My problem is that based on the original values (A, B) I can reproduce
the parameters for Li, Na,... of the standard Amber database.
However, I cannot reproduce the values of Mg and Ca.
Could anyone help me to find out why the values for Mg and Ca in the
current database are different from Aqvist's work.

Here a specific example

A=25 B=2.6,
R_min=1.137 and epsilon= 0.0183 (calculated using equation above),
R_min =  1.1370 and epsilon = 0.0183 (standard amber database)
-> perfect match as expected!

Mg (MG):
A=37 B=8.32,
R_min=0.787 and epsilon= 0.875 (calculated using equation above),
R_min =  0.7926 and epsilon = 0.8947 (standard amber database)

Ca (C0):
A=264.1 B=18.82,
R_min=1.326 and epslion= 0.4496 (calculated using equation above),
R_min =  1.7131  and epsilon = 0.459789 (standard amber database)

-> something is not right for Mg and Ca...

With kind regards,


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Received on Fri Oct 20 2017 - 04:00:01 PDT
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