Go to the directory which contains the MD simulation data.

Run the following:

$SCHRODINGER/run thermal_mmgbsa.py $BASE-out.cms -HOST 'localhost:X' -step_size Y -NJOBS Z

Where:

BASE="Name of trajectory"

X=Number of CPUs to use

Y=Every Nth frame to analyse

Z=Number of subjobs (Make sure Z>X, or Z=X)

Include options such as -lig_asl, -start_frame and -end_frame to specify the ligand that needs to be analysed, or have finer control of which frames are analysed.

Use the command below to save the outputs:

$SCHRODINGER/run thermal_mmgbsa.py $BASE-out.cms -HOST 'localhost:X' -step_size Y -NJOBS Z > MMGBSA-$BASE.txt