I have performed a protein-ligand simulation in desmond. I would like to perform mmgbsa calculations on the trajectory. Can anyone help me with the proper syntax of the command.
I tried "$SCHRODINGER/run thermal_mmgbsa.py -h" to know the syntax but could not figure out how to specify the input files.
Thanks.
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
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