<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:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 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;}
@font-face
{font-family:"Arial Narrow";
panose-1:2 11 6 6 2 2 2 3 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-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
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-AU" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The error itself is self explanatory, there are no 22 atoms in your protein structure, that suppose to be there. If you want to ignore those atoms when you
build your topology you can use the “–missing” option when you run pdb2gmx. But if you need all the atoms you better construct a complete protein structure using some other software before you run pdb2gmx.<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">Cheers,<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:"Arial Narrow","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial Narrow","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial Narrow","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial Narrow","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial Narrow","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial Narrow","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial Narrow","sans-serif";color:black">=========================================================<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">Emmanuel Birru<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">PhD Candidate<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">Faculty of Pharmacy and Pharmaceutical Sciences<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">Monash University (Parkville Campus)<br>
381 Royal Parade, Parkville<br>
Victoria 3052, Australia<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">Tel: Int + 61 3 9903 9187<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">E-mail:
</span><span lang="EN-US" style="font-family:"Calibri","sans-serif";color:#1F497D"><a href="mailto:firstname.lastname@monash.edu"><span lang="EN-AU" style="color:blue">emanuel.birru@monash.edu</span></a></span><span lang="EN-US" style="font-family:"Calibri","sans-serif";color:black">
</span><span style="font-family:"Calibri","sans-serif";color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black"><a href="http://www.pharm.monash.edu.au/"><span style="color:blue">www.pharm.monash.edu.au</span></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>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" 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>Seera Suryanarayana<br>
<b>Sent:</b> Monday, 4 June 2012 3:52 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Regarding error<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Dear all gromacs users,<br>
<br>
<o:p></o:p></p>
<div id=":5a">
<p class="MsoNormal" style="margin-bottom:12.0pt"> While i am running gromacs software i am getting following error.Let me know that error how to over come.<br>
<br>
Fatal error:<br>
There were 22 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology.<br>
<br>
Suryanarayana Seera,<br>
PhD student,<br>
Hyderabad,<br>
India.<br>
<br>
<o:p></o:p></p>
</div>
</div>
</body>
</html>