AMBER Archive (2004)

Subject: Re: AMBER: calcium van der Waals parameters

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Nov 22 2004 - 12:57:09 CST

> 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 ?

I didn't calculate them (did calculate and put the others in
the parm.dat files). Either it's an adjustment or a mistake.

Bill
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