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

[Mark Abraham]

----- 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


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  > 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.
 |
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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.

Mark



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