Group may be used for this job, and the first step is to prepare a PDB file for the hydrated ion.
In this case an NAMIDE record should precede the first amino-acid of the cyclic peptide, in the listing in the PDB input file.
On the opening page of PDB enter " superoxide dismutase " into the search box.
The format of pdb files generated by antechamber using the flag " -o pdb " is correct.
The new anisotropic tensors will be written to the coordinate file in the standard PDB format.
The problem with this is delivering to the reader the actual PDB file itself on which to execute the script.
The summary information gives an at-a-glance overview of the contents of each PDB entry including numbers of protein chains, ligands, metal ions.
The TOPS Atlas The atlas of topology cartoons was generated from the version of the PDB current on 1st July 1997.