From sudha.mrig from gmail.com  Sun May 18 11:22:13 2008
From: sudha.mrig from gmail.com (sudha.mrig@gmail.com)
Date: Sun May 18 12:31:02 2008
Subject: [Molecular-modelling] inorganic mol. docking
Message-ID: <58848cd9-2224-4dc4-b6f0-8124b1637fcf@w4g2000prd.googlegroups.com>

I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a
protein molecule. I could not locate any docking software which can
handle in organic molecule.  If anyone can help me in this regard.
Thanks

Sudha
From sunil.patel from camcellnet.com  Mon May 19 12:15:05 2008
From: sunil.patel from camcellnet.com (Sunil Patel)
Date: Mon May 19 13:56:55 2008
Subject: [Molecular-modelling] Re: Molmodel Digest, Vol 20, Issue 1
In-Reply-To: <200805191703.m4JH3JO01898@net.bio.net>
References: <200805191703.m4JH3JO01898@net.bio.net>
Message-ID: <859405740805191015r4771fb54w5812a2d93ad61ddd@mail.gmail.com>

Dear Sudha,

There are no real programs that "docks" inorganic molecules. The best way to
handle this is usually you place the molecule in the binding site, set up
the forcefields (ie Charges on the molecule), you can add restraints if you
know which residues/atoms it co-ordinates to and run MD simulation.

regards,

Sunil.


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> Date: Sun, 18 May 2008 09:22:13 -0700 (PDT)
> From: sudha.mrig@gmail.com
> Subject: [Molecular-modelling] inorganic mol. docking
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>
> I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a
> protein molecule. I could not locate any docking software which can
> handle in organic molecule.  If anyone can help me in this regard.
> Thanks
>
> Sudha
>
>
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From vpetrov from sco.com  Fri May 30 17:16:04 2008
From: vpetrov from sco.com (Vladimir Petrov)
Date: Fri May 30 18:46:27 2008
Subject: [Molecular-modelling] Re: inorganic mol. docking
References: <58848cd9-2224-4dc4-b6f0-8124b1637fcf@w4g2000prd.googlegroups.com>
Message-ID: <g1pub4$iql$1@aioe.org>

X-no-archive: yes
sudha.mrig@gmail.com wrote:
> I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a
> protein molecule.

I guess, you'd have to familiarize yourself with basics of General 
Chemistry first, and then decide how to dock ZnSO4 "in organic molecule" 
into the protein structure...