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

[Syed Azeem]

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

Azeem