AMBER: Calcium parameters

From: Lei Jia <>
Date: Fri, 02 Mar 2007 14:58:27 -0500

Dear Amber Users:

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.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Mar 04 2007 - 06:07:59 PST
Custom Search