[gmx-users] Re: Polyglycine PDB file.

C Johnson helstreak at hotmail.com
Mon Sep 13 00:06:16 CEST 2010

> I guess your pdb file has been damaged by a text editor (Word?). PDB 
> files are fixed format, you can not add or remove spaces at will. You 
> could try clicking together a peptide in Pymol or so, or drop the prodrg 
> output in Notepad (if you're on Windows). On mac or linux it should be 
> straightforward with text editors.

I copied the PRODRG PDB into vim, changed HETATM to ATOM and DRG to GLY and renumbered the residues.  I really don't understand what I could have done wrong.  Can you get the file to convert with pdb2gmx?
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