> ----- Original Message ----
> From: Bill Ross <ross.cgl.ucsf.edu>
> To: amber.scripps.edu
> Sent: Friday, December 22, 2006 11:51:07 AM
> Subject: Re: AMBER: Simulating proteins with calcium ion
>
> Sigma and R* are different mathematically - I believe sigma is
> where the potential curve crosses the zero point and R* is where
> it is at a minimum.
Yes, I distinguished them in my calculations: R_min = Sigma*2^(1/6). The vdw radius for Ca2+ is R_ca = R_min - R_oxygen.
> Also Aqvist values are derived for different
> combining rules than amber uses, so they need to be adapted.
> Discussion here:
>
> http://amber.scripps.edu/Questions/vdw.html
They look the same to me, and the link gives R_ca and epsilon as:
1.3264 0.44966
They are nearly identical to Kenley Barrett's calculation (
http://amber.ch.ic.ac.uk/archive/200504/0376.html ):
1.3262654 0.4496963
However, parm99.dat has:
1.7131 0.459789
Why is that?
Thanks,
Qing
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Received on Sun Dec 24 2006 - 06:07:41 PST
