Usually, when something like this happens after an unprotected sexual encounter, the first thought that comes to mind is that of an STD and rightly so as well. You go tested at the right time and your reports were negative. The doctor has also ruled out anything abnormal that might be pointing towards an STD.
However, the symptoms you mention having currently are not of an STD.
STDs present with fever, painful discharging ulcers or blisters, discharge of pus, frequency of urination and burning urination. All or most these symptoms need to be present in order to diagnose an STD.
Your symptoms are more likely due to dermatitis (eczema) or inflammation of the skin around the penis. I would suggest that you see your Dermatologist for a more clear opinion on this and in the interim use a combination of antibacterial and steroid twice a day like fusidin H cream.
Keep the area moisturized as much as you can and abstain from sexual intercourse for at least a week. Try not to wear nylon and polyester undergarments and use pure cotton only, all these measures will reduce friction and irritation of the sensitive skin.
Hope this helps.
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