AMBER Archive (2004)

Subject: Re: AMBER: calcium van der Waals parameters

From: cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Mon Nov 22 2004 - 11:10:30 CST

Thank you Dr Ross for your suggestions.
I had already read Aqvist paper but I had not seen the part on conversion of
the parameters in the FAQ.
Anyway, there is still a problem. In fact, I verified the parameters for
the ions found
in parm99.dat with the method exposed in the FAQ. The monovalent cations
are all OK,
but the two divalent cations whom parameters are said to be derived from
Aqvist parameters
(Ca2+ and Mg2+) have different values.
In parm99.dat, the values are :
r*(Ca2+)=1.7131 A and e=0.459789 kcal/mol
r*(Mg2+)=0.7926 A and e=0.8947 kcal/mol
When calculating them from Aqvist parameters, I obtained :
r*(Ca2+)=1.3264 A and e=0.44966 kcal/mol
r*(Mg2+)=0.787 A and e=0.875 kcal/mol

Do the parameters from Aqvist for Ca2+ and Mg2+ have been "re-optimized"
to deal with the
AMBER force-field ?

Thank you in advance for your answers,
Yours sincerely,
Fabien 

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

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