As a very beginner in using Linux/Python I didn't know why my downloaded lnx.exe didn't want to work. chmod command was the answer! chmod stands for "change mode", and it is used to define the way a file can be accessed. the u ser can r ead, w rite, ande x ecute it. chmod u+x hydronmr...lnx.exe Then, all you need is a file hydronmr.dat, like this example: 3.1-lysozyme !Name of molecule lysozyme31-nmr !Name for output file 6lyz.pdb !Strucutural (PBD) file 3.1, !AER, radius of the atomic elements 6, !NSIG 1.0, !Minimum radius of beads in the shell (SIGMIN) 2.0, !Maximum radius of beads in the shell (SIGMAX) 293., !T (temperature, K) 0.01, !ETA (Viscosity of the solvent in poises) 1, !Iflag (dipoles) -2.7126 !Gyromagnetic ratio of N: unit: 10^7 rad.s^-1.T^-1 1.02 !N-H distance, angstrom