AMBER Archive (2004)

Subject: AMBER: calcium van der Waals parameters

From: cailliez (
Date: Thu Nov 18 2004 - 10:53:23 CST

Dear all,

I would like to know how the parameters for the calcium ions which can be
found in parm99.dat have been obtained.
I read in amber manual that parameters for alkali ions have been derived
from those
obtained by Aqvist and adjusted to deal with TIP3P water molecules and
that these
parameters reproduced relative free energies of solvation and first peak
of radial distribution
for ion-OW in waters.
Did the same procedure have been used to derive calcium parameters (it
is written near the parameters
that they are adapted from Aqvist parameters) ? And did the relative
free energies of solvation
between calcium and alkali ions are well reproduced with these parameters ?

Thank you in advance for your answers,

Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail :
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					

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