Fix segfault on calling `make_ndx` without structure file

Fix segfault on calling `make_ndx` with only an index file input (no structure file).

Cause: Migration away from `t_blocka` in d7fca736 was not fully equivalent to previous code - natoms was not set. (`+1` comes from [this](d7fca736) )

Not sure how to emulate inputs at the interactive prompt to add a test for this.

Fixes #4717