From owner-chemistry ^%at%^ ccl.net Sun Sep 16 12:04:00 2007
From: "Kalyan chaitanya kalyanpulipaka%x%gmail.com" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL: query reg. docking followed by Dynamics
Message-Id: <-35163-070916120223-21647-dXCND8SpYMbDF50o93RD2w(a)server.ccl.net>
X-Original-From: "Kalyan chaitanya" <kalyanpulipaka^-^gmail.com>
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Date: Sun, 16 Sep 2007 21:32:15 +0530
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Sent to CCL by: "Kalyan chaitanya" [kalyanpulipaka*gmail.com]
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Hi all,

I have a doubt, I am now working on Docking and i learnt that M.Dynamics and
simulations would be very useful and efficient way of understanding how
exactly two molecules are interacting with each other, i have GROMACS,
TINKER and NAMD for the same purpose, but can you tell me-

1. Is it that we can see ligand and receptor coming together and trying to
fit with different conformations and finally binding itself with a stable
conformation.

2.can any one refer any publication papers who have done Docking followed by
Dynamics and simulations in showing the interactions.

3. how relaiable is M.Dynamics and simulations.

Thanks in advance,

Regards,

P.Kalyan

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<div id="mb_0">
<p>Hi all,</p>
<p>I have a doubt, I am now working on Docking and i learnt that M.Dynamics and simulations would be very useful and efficient way of understanding how exactly two molecules are interacting with each other, i have GROMACS, TINKER and NAMD for the same purpose, but can you tell me- 
</p>
<p>1. Is it that we can see ligand and receptor coming together and trying to fit with different conformations and finally binding itself with a stable conformation.</p>
<p>2.can any one&nbsp;refer&nbsp;any publication papers&nbsp;who have done Docking followed by Dynamics and simulations in showing the interactions.</p>
<p>3. how relaiable is M.Dynamics and simulations.</p>
<p>Thanks in advance,</p>
<p>Regards,</p>
<p>P.Kalyan</p></div>

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