<br><br>----- Original Message -----<br>From: NG HUI WEN <HuiWen.Ng@nottingham.edu.my><br>Date: Thursday, June 3, 2010 18:08<br>Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file<br>To: gmx-users@gromacs.org<br><br><span 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"><p> <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:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; margin-bottom:.0001pt; font-size:11.0pt; font-family:"Calibri","sans-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-compose; font-family:"Calibri","sans-serif"; color:windowtext;} .MsoChpDefault {mso-style-type:export-only;} @page Section1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.Section1 {page:Section1;} --> </style> <!--[if gte mso 9]><xml>
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</o:shapelayout></xml><![endif]--> <table><tbody><tr><td link="blue" vlink="purple" lang="EN-US"><p> </p><div class="Section1"> <p class="MsoNormal"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi,<o:p></o:p></p> <p class="MsoNormal"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></p> <p class="MsoNormal"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I’m a new gromacs user. I have encountered a problem with pdb2gmx where it automatically renumbers the residues in my pdb file. <o:p></o:p></p> <p class="MsoNormal"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></p> <p class="MsoNormal"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>For instance, the first residue in my protein F8 has become F1 – this affects all the residues in the protein, something I find rather inconvenient.<o:p></o:p></p> <p class="MsoNormal"><o:p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> </o:p></p> <p class="MsoNormal"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I’ve been searching the archive for previous posts which might have a solution to this but no luck so far. I might have been wrong. Many thanks for your help.</p></div></td></tr></tbody></table></p></span><br>I think you're out of luck. IIRC the facility you want is implemented in the development version, but not yet released. If you re-renumber by hand, then I suspect everything will be fine after that. grompp just needs something whose atom and residue naming and ordering matches the .top... how you produce that doesn't matter to it.<br><br>Mark