Hi,
Sorry for replying this late. I thought that maybe using MCPB.py is a
viable solution in this case and stopped following further updates posted
in the archive. Now, I understand the problems that I am going to face if I
don't take care of this problem that you have mentioned. Previously, I have
also tried the modeling by striping the crystal waters of the PDB and then
adding the suitable water box to see if any water molecule falls within the
coordination distance of zinc ion but none to avail. Can you please help me
with the ways about how to saturate the metal site with the water molecule?
That will be helpful.
with regards,
Satyajit Khatua
---------- Forwarded message ---------
Message: 7
Date: Thu, 22 Oct 2020 17:22:53 -0400
From: Pengfei Li <ambermailpengfei.gmail.com>
Subject: Re: [AMBER] Tri-coordination environment in zinc
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <2D91EE0A-7C34-4DFF-BA87-7654944421CE.gmail.com>
Content-Type: text/plain; charset=us-ascii
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 29 2020 - 23:00:01 PDT
