[gmx-users] Missing Residues

Justin A. Lemkul jalemkul at vt.edu
Sun Sep 20 21:26:06 CEST 2009

sunny mishra wrote:
> Hi All,
> My protein has lots of missing residues and in every chain there are 4-5 
> missing residues with atom name. I can see missing residues with the 
> help of Swiss PDB Viewer after I load the pdb file. I am very new in 
> Swiss PDB viewer and I would highly appreciate if anyone can let me know 
> how to fix the missing residues or add the missing residues in the 
> original PDB file using swiss pdb viewes before I start my simulations 
> in GROMACS. 

If you save the layer in Swiss PDBViewer, the .pdb file will contain the missing 
atoms that have been added.  Missing residues are entirely different issue.  You 
will have to use a program like Modeller or Loopy to re-build any missing residues.


> Thanks,
> Sunny
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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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