Pdb files generated in Marvin sketch

I am using Avogadro software 1.2 to optimize peptide structures (Drawn and saved 3D structures in Marvin Sketch (file .pdb ). After the procedures of Molecular Mechanics, I save them in PDB files again because I need them in PDB extension for the Molecular docking process. Nonetheless, Avogadro does not identify the amino acids and the atoms!
Please, would anyone have suggestions, critics, or advice?
Any help will be useful!!!

Because Avogadro 1.2 no longer is actively developed and maintained, use instead one of the installers of Avogadro 1.97 from the GitHub page suitable for your operating system. This covers Linux (by an app image), MacOS (dmg.zip), and Windows 64bit (exe.zip).

Please then amend your question by

  • a note; if the problem occurs, which version of Avogadro and OS you are using?
  • an input and output file representative of the problem you encounter e.g., via pastebin.com

Dear, Thomas
I appreciated your help. Thank you so much!!!

Kind regards

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