Dear Zoran,
Thanks for replying. Will try MCPB.py as you have suggested.
with regards,
Satyajit Khatua
Message: 9
Date: Sat, 19 Sep 2020 08:50:12 +0200
From: Zoran <zmatovic.kg.ac.rs>
Subject: Re: [AMBER] Tri-coordination environment in zinc
To: 'AMBER Mailing List' <amber.ambermd.org>
Message-ID: <caa6e0b6-2973-4936-a26a-b2e631e87346.kg.ac.rs>
Content-Type: text/plain; charset=UTF-8
Dear Satyajit,
MCPB.py would be just OK in your case.
Best,
Zoran
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On 19. ??? 2020. 06:36, at 06:36, 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 Sat Sep 19 2020 - 22:30:02 PDT
