[ENHANCEMENT] Increase fault tolerance of converter code

**Is your feature request related to a problem? Please describe.**
At the moment the are two scenarios of trajectory conversion failing where we may want to be more flexible and still create a usable output file:
1. The file is missing something that is required by the file format specification, but is not used by us. E.g. CASTEP `.md` file header, where the `MDFileConfigurator` requires the file header to be present, but then skips the entire header anyway.
2. One of the frames (especially the last one) is incomplete.

**Describe the solution you'd like**
While we need to inform the user about the problem, we should still make sure that we output a usable trajectory file containing all the previous frames and the atom database, etc.

**Describe alternatives you've considered**
For now I think that MDANSE converters should not fail where they don't have to. Other opinions can be added here.