Re: AMBER: Calcium parameters

From: Qing Zhang <>
Date: Fri, 2 Mar 2007 15:10:24 -0800 (PST)

----- Original Message ---------------------------------------------------- From: Lei Jia <> We are currently running simulations of a bypass polymerase Dpo4 with calcium ions at the active site. We used standard parm99 force field parameters for the calcium ion with a +2 charge. After the simulation, we saw the average coordination distance of the calcium ion is somewhat larger then the experimental value by about 0.3A. (simulated: ~2.6A, experimental ~2.3A). Did anyone observe the same problem? I wonder if there are some improved parameters in the current force field for calcium ion. Thank you very much. ------------------------------------------------------------------------------ Lei, Please look at these two threads discussing Ca2+ parameters: Sincerely, 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 Mar 04 2007 - 06:08:02 PST
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