Command Line Help

A description of the command line interface can be obtained by executing SZYBKI with the –help option.

prompt> szybki --help

will generate the following output:

Simple parameter list

  Execute Options
     -param : A parameter file


  Input Molecules
    Input Files Option 1 : Input molecule and optional protein
      -in : Name of the input molecule file. Aliases are -in and -i
      -protein : Name of the input protein file (not required)

  Input Files Option 2 : Ligand-protein complex
      -complex : Name of the input protein file with ligand(s)


  Output
    Output File Options
      -prefix : Replaces the default prefix for log, status, param and rpt
                files

    Explicitly specify individual file names
      -out : Name of the output molecular file


  Potential Function
    -ff : Force field to be used. Overwrites selection made with "-MMFF94S"


  Optimization
    -optGeometry : Specification of degrees of freedom used for optimization


Additional help functions:
  szybki --help simple      : Get a list of simple parameters (as seen above)
  szybki --help all         : Get a complete list of parameters
  szybki --help defaults    : List the defaults for all parameters
  szybki --help <parameter> : Get detailed help on a parameter
  szybki --help html        : Create an html help file for this program
  szybki --help versions    : List the toolkits and versions used in the application