----- Original Message ----------------------------------------------------
From: Lei Jia <leijia.nyu.edu>
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:
http://amber.ch.ic.ac.uk/archive/200612/0111.html
http://amber.ch.ic.ac.uk/archive/200701/0165.html
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)
qzhang.scripps.edu, www.qingzhang.info
=========================================
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Received on Sun Mar 04 2007 - 06:08:02 PST
