AMBER Archive (2007)

Subject: Re: AMBER: calcium parameter for GB

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Jan 18 2007 - 12:36:01 CST

> I am really confused about Ca2+ vdw radius. According to Aqvist, it should
> be 1.326. But in parm99.dat, it is 1.71. In different paper, different
> values were used. I am wondering which one should be the best in general
> cases.

The e parameter must also be taken into account, and the Aqvist
parameters must be adjusted for Amber combining rules. Search
old postings for Aqvist..

Bill
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