Required formats and default values of numerical and alphabetical parameters are listed e.g. in the quick help which can be printed to the screen by typing the name of the program at the command prompt:

$ mobywat

Calculation of hydration structures of molecular surfaces and interfaces
$ mobywat -x <value_x> -y <value_y> ...

Input files
-f       system.xtc      Trajectory file with frames
-pli     system.pli      Pool information file
-r       system_ref.pdb  Reference file
-tpy     system_tpy.pdb  Topology file

Input ranges
-l       x-y/[xy...]     Ligand range, atom serial numbers/chain IDs
-t       x-y/[xy...]     Target range, atom serial numbers/chain IDs
-w       x-y/WAT/Auto    Waters range, atom serial numbers/residue name/automatic

Parameters & defaults
-bmax    75.000          B-factor limit, A^2
-cls     IDa             Clustering algorithm, IDa/IDe/POS/MER
-ctol    1.000           Clustering tolerance, A
-dmax    3.500           Distance limit, A
-m       Prediction      Program mode, Analysis/Prediction
-mtol    1.500           Match tolerance, A
-n       0-10            Frame range, x-y
-ptol    2.500           Prediction tolerance, A
-ptop    50.000          Top cut of short prediction list, %
-v       Silent          Verbosity, Silent/Verbose/Diagnostic

For detailed instructions, please visit the web site at !