[gmx-users] Re: Polyglycine PDB file.

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 13 00:08:45 CEST 2010

C Johnson wrote:
>  > 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?

If you simple replace HETATM with ATOM, i.e.:


you shift all columns left by two characters.  This is probably why, instead of 
reading GLY, pdb2gmx is reading Y only.  The proper replacement would be:

:1,$s/HETATM/ATOM  /

Note the two trailing spaces after ATOM.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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