If you are legally separated as of the last day of the year then you can file as single.
If you are married but didn't live with your spouse for the last half of the year and you have a qualifying child you can file as head of household.
If you must file married filing separately and you do not know your spouse's AGI and can't get it from them then yes, you should enter zero.
Here is more information on Married Filing Separately
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