[gmx-users] pdb2gmx renumbers the residues in my pdb file

Mark Abraham mark.abraham at anu.edu.au
Thu Jun 3 10:27:29 CEST 2010

----- Original Message -----
From: NG HUI WEN <HuiWen.Ng at nottingham.edu.my>
Date: Thursday, June 3, 2010 18:08
Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file
To: gmx-users at gromacs.org

      <!--  /* 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;} -->   -----------------------------------------------------------

  > Hi,
  > I’m a new gromacs user. I have encountered a problem with pdb2gmx where it automatically renumbers the residues in my pdb file. 
  > 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.
  > 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.

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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100603/1ca9f6f9/attachment.html>

More information about the gromacs.org_gmx-users mailing list