<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 12 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal;
font-family:"Arial","sans-serif";
color:windowtext;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:595.3pt 841.9pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">You will have to check the paper that describes the FF
<a href="http://dx.doi.org/10.1002/Jcc.20090">http://dx.doi.org/10.1002/Jcc.20090</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">However, don’t believe carbon dioxide has been parameterised within the FF, the OM is the carboxyl oxygen i.e. –C<b>O</b>OH<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best idea is to search to see if someone else has parameterised for carbon dioxide with that FF. Otherwise you are going to have to spend a fair amount of
time sorting it out yourself.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div style="border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt">
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>Junfang.Zhang@csiro.au<br>
<b>Sent:</b> Tuesday, 1 May 2012 5:53 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Re: CO2/gromos53a5<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy">Dear Gromacs users<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy">Which carbon and oxygen in gromos53a5 is the carbon and oxygen in CO2?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy">OM is oxygen in CO2. Am I right?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy">Thanks<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy">JF Zhang<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
</div>
</div>
</body>
</html>