Issue using mk_prepare_receptor.py to prepare large pdbs

[allisonbarkdull]

I am having issues using meeko to prepare a receptor with a large number of atoms.
for example, running mk_prepare_receptor.py -i 7khr.pdb --write_pdb 7khr_APB.pdb -j 7khr_APB.json -a yields a somewhat compromised output because the input has so many atoms that the serial number took one too many digits and shifted everything one column.