AMBER Archive (2007)

Subject: Re: AMBER: calcium parameter for GB

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Wed Jan 24 2007 - 11:33:24 CST

> >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) qzhang_at_scripps.edu, www.qingzhang.info =========================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu