If you hover the mouse over the line with the red exclamation mark a tooltip should appear which will tell you what the error is.

With msms.txt files it is usually necessary to put the mqpar.xml and modifications.txt files in the same folder as the msms.txt file so that BiblioSpec can understand the modifications.

If you are still having trouble you can send us your files and we can try to figure it out.

Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url

--Nick