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I have an output from induced fit docking (IFD) in Maestro. I want to calculate the MM-GBSA for the output obtained from IFD in Maestro (Schrodinger) for which poseviewer file (.pv.maegz) is required. Can someone tell me how to export/convert .maegz file in .pv.maegz format. Or, how can I split my complex in ligand and receptor files. I tried using the schrodinger script for the conversion but that did not work.

Any help would be appreciated.

Thanks in advance,

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  • $\begingroup$ To do MM-GBSA in the Shrodinger suite you don't need pose file. $\endgroup$
    – Camps ♦
    Apr 18, 2022 at 18:17
  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Apr 18, 2022 at 20:48

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From the Knowledge Base post in the Schrodinger site:

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 the -ligand option that will allow you to specify the part of the input complex that should be considered as the ligand for the MM-GBSA calculation

Alternatively, the complex file can be converted to a poseviewer file before running the job. 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

Use the -mode split_pv option.

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