On Tue, Mar 04, 2014, Gmail2 wrote:
>
> In my structure, a zinc is connected to the nitrogens of three
> histidines and a water. The structure should be simulated with Zn bound
> to three deprotonated (negative) histidines and a water.
Please be aware that what you are proposing goes against a lot of "received
wisdom", which holds that histidines bound to zinc should be neutral.
Certainly having *three* deprotonated histidines would be most questionable.
There are plenty of zinc protein experts who can chime in here: both on the
general question, and on whether there are any experimental determinations of
a histidine pKa bound to a zinc ion.
You probably don't need to do a bunch of new parameterizations: there is
plenty of published work on how to model MMP-like active sites with Amber:
Lin & Wang, JCTC 6: 1852, 2010
Peters et al, JCTC 6: 2935, 2010
A google search on "zinc protein amber parameters" will yield yet more info.
...good luck....dac
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Received on Tue Mar 04 2014 - 11:00:03 PST
