Article ID: 1484 - Last Modified: June 7, 2011
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
$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:
Keywords: Prime MM-GBSA MMGBSA
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