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Article ID: 146 - Last Modified:

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

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. The best way to do this is with the command

run scriptname.py [options]

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

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