How are Prime MM-GBSA calculations carried out, and what solvation model is used? Is this described somewhere in the literature?

A number of calculations (energy calculations and energy minimization) are performed during an MM-GBSA job, and you can see them all if you submit a job from the command line, using the -keep and -LOCAL options:

$SCHRODINGER/prime_mmgbsa -keep -LOCAL [other options] pose-viewer file

Here are the jobs that are run:

Receptor alone (minimization)
Ligand alone (minimization)
Receptor-ligand complex (minimization)
Ligand extracted from optimized receptor-ligand complex (energy calculation)
Receptor extracted from optimized receptor-ligand complex (energy calculation)

All Prime energy components (Coulomb, vdW, solvent, etc) are reported in (and can be extracted from) the individual job log files.

Prime MM-GBSA uses the SGB solvation model, with some customizations. For more information, see Article 1492.

For further information, see the Prime publications on our website:

http://www.schrodinger.com/productpublications/14/14/

Keywords: Prime MM-GBSA MMGBSA

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