Is it ok to take l lysine with amoxicillin?

Yes: Wise to ask to be sure. L-Lysine is a very benign substance, an amino acid that we get in our diet every day. It's not known to interact with pharmaceuticals except one type- aminoglycoside antibiotics like gentamycin. But it's perfectly safe to take Lysine with Amoxicillin. It's also wise to take probiotics, esp. Sacchromyces boulardii. See https://umm.edu/health/medical/altmed/supplement/lysine