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I took him to the vet he said the turtle has abscess and requires an operation I want to know if there is any other way I can remove the abscess by perhaps some medicine or cream??

Maybe antibiotics, but this is usually a simple surgery for a vet. Usually anesthetics aren't required either. Make sure that it's a qualified herp vet.

How do I give him the capsule do i open and mix it the water or just give it to him normally?

Antibiotic dosage depends on severity of illness, size/age of the turtle and medication. This is something the vet needs to prescribe after an exam.