Hi,
Echoing Dave's comment it is unlikely that you have three deprotonated His residues. In the papers mentioned force fields for the protonated coordination you are working on is reported. If you want to do this from scratch you can use MCPB in AmberTools. Good luck! Kennie
On Mar 4, 2014, at 1:58 PM, David A Case <case.biomaps.rutgers.edu> wrote:
> 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 - 13:30:02 PST
