Re: AMBER: calcium parameter for GB

From: Qing Zhang <>
Date: Wed, 24 Jan 2007 09:33:24 -0800 (PST)

> >Could you tell me how r=1.6 is derived. > > As J. Chem. Soc. Faraday T. 94:1603–1611. indicates, the r=1.600 was chosen to maintain > reasonable geometry > around the metal centres during energy minimisation of the EF-hand. My simulations with r=1.367, > 1.7131 , 1.50, 1.55 and 1.60 indicate the later (r=1.60) is the best value. > I am not sure whether the value is accurate, but no other choice for me now. Thanks, Ji-Lai. I am also interested in knowing how you define a reasonable geometry. Does it means that Ca2+ should have 6-8 coordinated oxygens and the average distance of the oxygens to Ca2+ is around 2.4 Angstrom? I also wonder why the geometry should be maintained in minimization not in dynamics. Thanks, Qing ========================================= Qing Zhang, Ph.D. The Scripps Research Institute 10550 North Torrey Pines Road, mail MB-5 La Jolla, CA 92037 858-784-2333 (Lab), 917-509-3182 (Cell), =========================================
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Received on Sun Jan 28 2007 - 06:07:09 PST
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