[AMBER] Discrepancy in Ca++ Vdw parameters considering two Amber data sources - please comment

From: Marek Maly <marek.maly.ujep.cz>
Date: Tue, 19 Jul 2011 16:33:58 +0200

Hello all,

in actual parm99.dat one can find regarding Ca++ Vdw parameters this line:

C0 1.7131 0.459789 Ca2+ Aqvist JPC

and here is content of FRCMOD file regarding Ca++ and Mn++ Amber
contributed parameters
(see http://www.pharmacy.manchester.ac.uk/bryce/amber#ion )

Ca2+ and Mn2+ vdw parameters from Concanavalin A study
MN 55.00 0.00
KA 40.00 0.00

    MN 1.6900 0.0140
    KA 1.7900 0.0140


As one can see values of r_Vdw are similar in both cases ( C0 and KA )
in case of well depth (epsilon) there is really huge difference 0.459789
versus 0.014 (cca 33 x bigger in
case of C0 comparing KA).

How can one understand this discrepancy which has probably roots in
different derivation of the VdW parameters in each case ?

Should one for example use KA atom type/parameters for simulations where
Ca++ ions are coordinated to "Concanavalin A" or
to another protein with similar binding site and for the rest cases ( e.g.
Ca++ ions fluctuating in the water and/or interacting with
quite different protein binding sites (than in case of Concanavalin A) or
with another molecules (e.g. polymers) ? ) is better
to use C0 atom type/Vdw parameters ?

Is there eventually available relevant article regarding above mentioned
"Concanavalin A study" ?

    Thanks a lot in advance for any comment !

       Best wishes,


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Received on Tue Jul 19 2011 - 08:00:04 PDT
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