Running SiteMap from the Command Line

SiteMap can be run from the command line with the sitemap command. For general information on running jobs from the command line, see Running Schrödinger Applications from the Command Line.

The syntax of the sitemap command is as follows:

sitemap [options] [-prot file.mae] [-i jobname.in]

The principal arguments are described below.

-j[ob] jobname

Specify the job name. jobname is used to make some file names unique.

 
-prot file.mae

Specify protein file in Maestro format, compressed or uncompressed. Required, either on the command line or in a command input file.

 
-i jobname.in

Specify command options as keywords in a command input file.

On Windows, you can run this command in a Schrödinger Command Prompt window, which you can open from the Start menu.

The job name is the determined by first of the following sources:

  • the -j[ob] option
  • the stem of the input file name as specified with -i
  • the stem of the protein file name as specified with -prot