Hi,
Can you suggest to me any other tool to do so?
with regards,
Satyajit Khatua
---------- Forwarded message ---------
Message: 6
Date: Sun, 1 Nov 2020 10:35:31 -0800
From: Bill Ross <ross.cgl.ucsf.edu>
Subject: Re: [AMBER] Tri-coordination environment in zinc
To: amber.ambermd.org
Message-ID: <eec483ff-eba4-ed99-e6d4-0dc151e5a5e3.cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
Yes. It's harder to do with xleap than other graphic editors, but still
might only take a few minutes.
Bill
On 11/1/20 9:38 AM, SATYAJIT KHATUA wrote:
> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Nov 02 2020 - 21:30:02 PST
