Article ID: 1568 - Last Modified: January 31, 2012
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, available from the Script Center on our web site. Use the following command:
$SCHRODINGER/run pv_convert.py -h
to see usage and options. You will want to use the -p option.
Keywords: Prime, MM-GBSA, MMGBSA
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