Protonated state of HIS

I am trying to use the molprobity to find the protonated state. But for some reason it is always telling me the histidine is HIS+ (even when I know for a fact its not).
I put the reduce file in ~/software/bin/ like it says to do.
Do you know why?

It is simply not perfect - only makes an educated guess based on the hydrogen bond network around the HIS.

There are other tools to do this, e.g. propka

For use in HADDOCK, you can also manually define the protonation state of the various HIS.

Its wrong even when its specifically has only a hydrogen on HD1 (for example when I use an NMR structure… ) and also when following your tutorial on haddock I used the same structure and only got HIS+
Can there be any ithe reason?

בתאריך יום ה׳, 3 באוג׳ 2023, 15:01, מאת Alexandre Bonvin via BioExcel ‏<>:

It is simply not a full-proof method.

If you know your protonation state you can manually define it in the server.