Fix paths of files

[Justin Lorieau]

The following works:

ml pa -i 2lwa_1.pdb 2lwa_2.pdb 2lwa_3.pdb -d G8A_comparison.inp -o ./temp.out

The following does not:

ml pa -i 2lwa_1.pdb 2lwa_2.pdb 2lwa_3.pdb -d G1E_pH_7_G8A_comparison.inp -o temp.out