From owner-chemistry@ccl.net Wed Feb 23 13:30:00 2011
From: "sadia zafar diya.khan.05]=[gmail.com" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL: binding of ligand on protein in water box
Message-Id: <-44005-110223120206-28643-8qW4va+Oe/qbU1MzDUodJw-$-server.ccl.net>
X-Original-From: sadia zafar <diya.khan.05(0)gmail.com>
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Date: Wed, 23 Feb 2011 22:02:00 +0500
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Sent to CCL by: sadia zafar [diya.khan.05[*]gmail.com]
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Respected Sir!
                       I want to add a ligand molecule (sugar chain) on my
protein. I have been searching for its procedure in the archive of the NAMD
mailing lists and also on the web but could not find methodology.
Can you please guide me that how I can perform protein-ligand simulation?
Secondly is it better to take a start by initially adding the ligand to the
protein structure i.e. making a protein-ligand complex and then running
simulations on it or should I do simulation of the protein alone and then do
the addition of ligand molecule?

Thanks.

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Respected Sir!<div>=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 I want to=
 add a ligand molecule (sugar chain) on my protein. I have been searching f=
or its procedure in the archive of the NAMD mailing lists and also on the w=
eb but could not find methodology.</div>
<div>Can you please guide me that how I can perform protein-ligand simulati=
on?=A0</div><div>Secondly is it better to take a start by initially adding =
the ligand to the protein structure i.e. making a protein-ligand complex an=
d then running simulations on it or should I do simulation of the protein a=
lone and then do the addition of ligand molecule?</div>
<div><br></div><div>Thanks.</div>

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