'Using Modeller to create a new pdb file containing two pdb files and a linker

I need to create a new pdb file containing two pdb files and a linker with 12 Glycine.

I generated this pdb file using Modeller, but the structure looks weird to me, because it seems that the linker and the second pdb file do not show appropriate secondary structure!

Could you please help me solving this issue?

pdb-filesvmd


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