<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear all; </div><div> As you all know, in all of the force fields in Gromacs package, G,C,A and T are known. In your opinion, what should I do in case of 8-OxoG? How to obtain parameters needed for this new residue?</div><div> Thank you </div><div> B.Mehrazma</div> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Sunday, December 25, 2011
10:58 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Fw: modifying the mutated DNA parameters<br> </font> <br>
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On 12/25/2011 6:04 PM, banafsheh mehrazma wrote:
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; ">
<div><span>Dear Mark;</span></div>
<div><span>Thank you for your instant reply. You are right, but
in my case, there is a residue 8-OxoG (oxidized G). As you
know, in all of the force fields in Gromacs package, G,C,A
and T are known. In your opinion, what should I do in case
of 8-OxoG, to obtain parameters needed for this new residue?</span></div>
<br>
</div>
</blockquote>
<br>
You're assuming that you need a new atom type and/or bonded
parameters for your force field. You have to determine whether that
is true, yet.<br>
<br>
Mark<br>
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