The reason (per DH's doctor) that you shouldn't take melatonin with Zoloft is because melatonin interferes with serotonin production. Since Zoloft is an SSRI, it functions by regulating serotonin levels in the brain, and messing with that even more can cause serious dips and spikes in serotonin levels, which can lead to Serotonin Syndrome.
DH had the opposite issue with Zoloft - it turned him into a zombie. He had no emotions and was asleep just about every minute he wasn't at work, and he had a hard time staying awake at work.
Hang in there, your body may regulate itself after a few weeks on the meds. If not, your doctor can always adjust the dose or try a different drug.
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