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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)

epsilon=B^4/(4*A^2)

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

Li:

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,

Nadine

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

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

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)

epsilon=B^4/(4*A^2)

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

Li:

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,

Nadine

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

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

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