The format of pdb files generated by antechamber using the flag " -o pdb " is correct.
The TOPS Atlas The atlas of topology cartoons was generated from the version of the PDB current on 1st July 1997.
Group may be used for this job, and the first step is to prepare a PDB file for the hydrated ion.
The summary information gives an at-a-glance overview of the contents of each PDB entry including numbers of protein chains, ligands, metal ions.
In this case an NAMIDE record should precede the first amino-acid of the cyclic peptide, in the listing in the PDB input file.