Hi Satyajit,
The answer is yes. MCPB.py can deal with various coordination modes. One issue will raise because you have two water molecules coordinated to the same metal ion, please check the second last paragraph in this tutorial: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm> about how to solve this issue.
Hope it helps,
Pengfei
> On Jul 30, 2019, at 1:22 AM, SATYAJIT KHATUA <satyajitkhatua09.gmail.com> wrote:
>
> Dear AMBER users,
>
> Recently, I am modelling the active site of HCA-IX where the metal ion has
> the coordination of 5 with three histidine residues and two water
> molecules. By searching the related references, I came to know that five
> coordination site of zinc can be modelled using MCPB.py tool. I have used
> it previouly for modelling of ligand bound enzymes but all of them had
> tetra coordination. So, is it possible to model a penta coordination
> without any ligand and two water molecules are connected to the metal
> center? any help in this context will be appreciated.
>
>
> Thanking you,
>
> Satyajit Khatua
> Dept. of Chemistry
> IIT Kharagpur, India.
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Received on Wed Aug 07 2019 - 20:00:02 PDT
