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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
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