Hello all,
in actual parm99.dat one can find regarding Ca++ Vdw parameters this line:
C0 1.7131 0.459789 Ca2+ Aqvist JPC
1990,94,8021.(adapted)
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
MASS
MN 55.00 0.00
KA 40.00 0.00
NONB
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 )
while
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,
Marek
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Received on Tue Jul 19 2011 - 08:00:04 PDT
