[gmx-users] Reg: creation of separate chains in .pdb file

Syed Azeem syedazeemullah186 at gmail.com
Mon May 29 14:00:10 CEST 2017

Hey all,

I simulated a protein-peptide docked complex. Post simulation, I
created an index file selecting only the Protein Group
(protein-peptide complex). Then using editconf, I created a .pdb file
for the same.

When I view the prtn.pdb file, only the protein is available but not
the peptide. Still the prtn.pdb file has coordinates for peptide as
well. The pdb file also lacks a chain identifier, which was present in
the initial structure.

How to overcome this?

Thanks in advance


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