Hi.

If you have specific questions or doubts then I am sure you will get a lot of answers. For the overall procedure and step by step guide of how to perform MM-GBSA calculations using Schrodinger, you will have to consult the Prime user manual and How-to guide available on Schrodinger website. They explain the entire process in great detail. You will also find many detailed step by step tutorials on the Internet with a simple google search, like this one (http://gohom.win/ManualHom/Schrodinger/Schrodinger_2015-2_docs/maestro/help_Maestro/prime/prime_mmgbsa_panel.html). You can try on youtube as well.

thank you very much...

For MM-GBSA calculation, use Prime module of Maestro not Glide. You can directly import the output file of the docked complex and add it to calculate MM-GBSA. Or alternatively you can define the protein and ligand to calculate MM-GBSA.

As Glide is basically for docking calculations the docked complex output from Glide can be used as input in the Prime module for energy calculation (MM-GBSA). the output of this process will be located in the selected directory. The folder consists of 6 files of which the out.csv file (excel file) contains all the energies of the complex. Let me know if this helps.

Following

@mahbudul himel thank you very much

I have a problem with running the MM-GBSA calculations. I use the xp docking file (pose viewer file) and keep the parameters on default settings and run it, unfortunately, the process fails after few seconds.

Any idea why this does happen?

Haider Almuqdadi

Please ensure that the file names are checked for any spaces, as they could potentially cause your job to fail once it has started.