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??
python $HOME/convert.py $basename.forces > $extname.vtk

Not sure I understood what you want...

Try:
extname=$(echo "$file" | sed 's/[^0-9]*\([0-9]*\)\.\(.*\)/\2\1/')

It would help if you would show us some sample input that your sort command is not sorting the way you want.

Note that the sort key specification -k1 tells sort to sort a line with the sort key...