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On 12/24/2011 10:41 PM, banafsheh mehrazma wrote:
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--- On <b>Sat, 12/24/11, banafsheh mehrazma <i><a class="moz-txt-link-rfc2396E" href="mailto:bmehrazma@yahoo.com"><bmehrazma@yahoo.com></a></i></b>
wrote:<br>
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From: banafsheh mehrazma <a class="moz-txt-link-rfc2396E" href="mailto:bmehrazma@yahoo.com"><bmehrazma@yahoo.com></a><br>
Subject: <br>
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Date: Saturday, December 24, 2011, 3:39 AM<br>
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<div>To whom it may concern;</div>
<div>I am willing to study a damaged DNA which
has a 8-oxoG as the lesion (the Carbon 8 in
guannine is oxidized.). I have the following
questions;</div>
<div>1) Should I change the sigma and epsilon
parameters in the force field that I want to
work on? and how?</div>
<div>2) Should I change the bonded parameters
in the force field? and how?</div>
<div>3) The new charges for the lesion are
obtained from Gaussian package; where can I
mention the modified charges?</div>
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You need to consider your molecule in the light of the existing atom
and bonded interaction types for the force field you have chosen.
Maybe you need new ones, maybe not. For 3, you should consider the
advice here <a
href="http://www.gromacs.org/Documentation/How-tos/Parameterization">http://www.gromacs.org/Documentation/How-tos/Parameterization</a>
(so your Gaussian-based charges may not be useful at all), and <a
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a>.
All of the above will need a thorough knowledge of chapter 5 of the
manual.<br>
<br>
Mark<br>
<br />--
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