<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><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><div><span> Thank you</span></div><div><span> B.Mehrazma</span></div><div><br></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> banafsheh mehrazma <bmehrazma@yahoo.com><br> <b><span style="font-weight:
bold;">To:</span></b> gmx-users@gromacs.org <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, December 24, 2011 3:11 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] Fw: modifying the mutated DNA parameters<br> </font> <br>
<div id="yiv14393770"><table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td valign="top" style="font:inherit;"><br><br>--- On <b>Sat, 12/24/11, banafsheh mehrazma <i><bmehrazma@yahoo.com></i></b> wrote:<br>
<blockquote style="PADDING-LEFT:5px;MARGIN-LEFT:5px;BORDER-LEFT:rgb(16,16,255) 2px solid;"><br>From: banafsheh mehrazma <bmehrazma@yahoo.com><br>Subject: <br>To: gmx-users@gromacs.org<br>Date: Saturday, December 24, 2011, 3:39 AM<br><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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<div>Thank you for your regards</div>
<div>B.Mehrazma</div></td></tr></tbody></table></div></blockquote></td></tr></tbody></table></div><br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br> </div> </div>
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