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How do I run Schrödinger applications from the command line under Windows?

From Suite 2011 on, you can run most applications in a Schrodinger Command Prompt window, which you can open from the Start menu (Start → All Programs → Schrodinger-year → Schrodinger Command Prompt). This is a DOS shell that has been configured with all the necessary settings to run Schrödinger software. You do not need to include the path to the application to run it. For example, you can run LigPrep by just typing ligprep with the appropriate arguments at the command prompt. Likewise, you can just type pdbconvert with the appropriate options to use the PDB conversion utility.

If you want to run Unix commands, type sh in this window to start a lightweight Unix shell, or simply precede the Unix command with sh. The set of Unix commands is limited, so you might not be able to do everything that you can do on Linux

You can also run Python scripts in this window, such as scripts obtained from the Script Center. The best way to do this is with the command

run [options]

The run command sets up the environment for the Python script and then runs it.

For earlier releases, the easiest option for running from the command line under Windows is to use the SchrodingerShell utility, located in the Schrodinger installation directory. Browse to this directory and launch the SchrodingerShell application with a double click. This utility starts the same lightweight UNIX-like shell as in Suite 2011, with the environment correctly configured to run jobs. You can use it for Unix commands and for Python scripts, as described above.

Keywords: Windows, command line, Schrodinger, Python

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