You have to include an entry for each parent in the Ped file even if they are missing. Also, even if a parent is missing you should give them a non-zero ID if the other parent isn't missing. So if the parent (father) is missing from family 1 it currently looks like this:
Family1 Sib1 Father0 Mother8 1
And you need to change it such that the missing father for the group still gets a unique ID:
Family1 Sib1 Father7 Mother8 1
In addition, you need to add the father to your pedigree file:
Family1 Father7 0 0 1
Notice that both parents are missing for Father7 so you can set both to 0 and there isn't the expectation that they will be listed in the Ped file somewhere.