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.
Lei
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Received on Sun Mar 04 2007 - 06:07:59 PST
