Hi Satyajit,
For this case maybe it is better for you to saturate the metal site first with an additional water before the MCPB.py modeling. If the metal site is not saturated, it could be challenging to get meaningful results for the quantum calculations.
Pengfei
> On Sep 19, 2020, at 12:36 AM, SATYAJIT KHATUA <satyajitkhatua09.gmail.com> wrote:
>
> Dear Users,
>
> Anyone here have worked with tri-coordination environment on zinc in protein?? Recently, I am working on a superantigen protein that contains a tri-coordinated environment (two bound His- and one Asp-) on zinc. Usually zinc possess a tetra-coordination. In crystallography paper, they told that possibly there is a water molecule on fourth position although they didnt find any signature on electron density map. So can someone give some inputs about the parameterization of this zinc coordination through amber force fields?? Any suggestions about some tutorials or papers in this regard will also be appreciated.
>
> Thanks in advance,
> Satyajit Khatua
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Received on Thu Oct 22 2020 - 14:30:04 PDT
