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Article ID: 1568 - Last Modified: August 18, 2014

How do I run Prime MM-GBSA on a complex in a Maestro file from the command line?

The command to use for Prime MM-GBSA is:

$SCHRODINGER/prime_mmgbsa [ options ] structure_file.mae[gz]

Run with -h to see all options. Note that the structure file cannot be a complex. It has to have the form of a Glide pose viewer file, with the receptor and ligand separated. You can generate the pose viewer file by importing the complex to Maestro, splitting the entry into receptor and ligand and then exporting again. There is also a script that you can run from the command line, pv_convert.py. Use the following command to see usage and options:

$SCHRODINGER/run pv_convert.py -h

You will want to use the -p option.

Keywords: MMGBSA

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