Missing Ions from Clusters

According to the haddock manual Haddock can deal with ions. In my runs, I used the following ions in addition to the proteins being docked, placed in one of the files:

HETATOM 954 MG+2 MG2 M 33 -10.214 -2.615 19.293 0.81 5.49
HETATOM 955 MG+2 MG2 M 34 -6.004 1.802 13.778 0.60 20.66

The section was prefixed and suffixed by “TER”'s. The Haddock webserver added the run to the queue without error, but all clusters returned did not contain the ions within the
resultant PDB’s.

What could I be doing wrong?

The only thing I’ve noticed is wrong is that the PDB file does not terminate with an “END”, and the ions are the last chain, but that seems circumstantial at best.

Potentially valuable information: the ions were present in an input PDB marked as ‘DNA’. Would this have stopped the exporting of all non-base-pair residues? Would this work if it were in a file marked as protein?

Are you using the web server or a local version?

Also the ions in that case should have the same chainID as the protein