Hi,
Thanks for replying. Here, I am talking about one water intending to
satisfy the metal site coordination. Can I place the water by hand using
the leap editor?
with regards,
Satyajit Khatua
---------- Forwarded message ---------
Message: 7
Date: Thu, 29 Oct 2020 23:59:57 -0700
From: Bill Ross <ross.cgl.ucsf.edu>
Subject: Re: [AMBER] Tri-coordination environment in zinc
To: amber.ambermd.org
Message-ID: <9c0e181c-eae2-73db-90f6-a9f4970b1131.cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
If we're just talking about a few waters, why not just place them by hand?
Bill
On 10/29/20 10:39 PM, SATYAJIT KHATUA wrote:
> 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 Sun Nov 01 2020 - 10:00:02 PST
