Hi there,
You can execute a program via a PRTG notification. Assuming that you only have a small script that simply restarts the server please note that, without any further configuration, the script is been executed under the security context of the PRTG Probe service.
In your tests, where you've executed the script manually, it ran under your security context, which is most commonly the crux here.
To solve the issue, please navigate in PRTG to Setup | Account Settings | Notification Templates and select the desired template. Here, scroll all the way to Execute Program and make sure to have proper credentials next to the script in place.
For further information, please check the corresponding manual article:
Notification Templates | Execute Program
Best,
Sebastian
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