Prime User Manual - ISP

Table 10.1. Options for the prime_mmgbsa command
Option Description
Chapter 10: Prime MM-GBSA
-b jobname Use alternative job basename. Default is to use the input file basename.
-cmae Use atomic partial charges from the input Maestro file in simulations
-extdiel value Set the external dielectric to value.
-h Print help message and exit
-intdiel value Set the internal dielectric (including the membrane) to value.
-keep Save all minimized ligand, complex, and protein structures (default is to save
only minimized protein-ligand complexes)
-lstrain Include an estimate of the ligand strain energy in the output
-membrane Use the Prime implicit membrane model in protein and complex simulations
-n subjobs Number of subjobs to run.
-rflex file File listing protein residues to be treated flexibly. The residues are specified
in the format chain:residue.
-v Print version information and exit
The output Maestro structure file includes a number of properties, which are described in
Table 10.2.
Table 10.2. Output properties from a Prime MM-GBSA calculation.
Property Description
Prime Coulomb Coulomb energy of the complex
Prime Covalent Covalent binding energy of the complex
Prime vdW Van der Waals energy of the complex
Prime Solv SA Solvation surface area of the complex
Prime Solv GB Solvation energy of the complex
Prime Energy Prime energy of the complex
Prime MMGBSA
Complex Energy
Prime MMGBSA Ligand
Energy
Prime MMGBSA
Receptor Energy
MMGBSA energy of the complex
MMGBSA energy of the free ligand
MMGBSA energy of the uncomplexed receptor
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