iterating over files

[Gribouillis]

You could simply use Python's format method

template = """\
TEMPOP /home/c.blanes/FlexAID2/FlexAID_Output
PDBNAM /home/c.blanes/FlexAID2/Processed_files/receptor.inp.pdb
INPLIG /home/c.blanes/FlexAID2/Processed_files/{ligand}.inp
RNGOPT LOCCLF /home/c.blanes/FlexAID2/Binding_sites/binding_site.pdb
OPTIMZ 9999 - -1
OPTIMZ 9999 - 0
OPTIMZ 9999 - 1
OPTIMZ 9999 - 2
OPTIMZ 9999 - 3
OPTIMZ 9999 - 4
...
"""

names = ['foo', 'bar', 'baz']

for idx, name in enumerate(names, 1):
    with open('CONFIG{}.inp'.format(idx), 'w') as outfile:
        outfile.write(template.format(ligand=name))