MMGBSA Calculation from Schrodinger thermal_mmgbsa.py

2023-05-04

‚Äč

Run the script

Go to the folder that have the out.cms trajectory file. You can check the existing files by ls

Then run the script-

where:-

  1. xx-out.cms=simulaiton out file >
  2. Y=GPU
  3. YY=The simulation frames gap
  4. Z=Number of prime subjobs to create (Make sure Z>Y, or Z=Y)
$SCHRODINGER/run thermal_mmgbsa.py xx-out.cms -HOST 'localhost:Y' -step_size YY -NJOBS Z

Example:

$SCHRODINGER/run thermal_mmgbsa.py desmond_md_job_2-out.cms -HOST 'localhost:4' -step_size 20
thermal_mmgbsa start

It will generate a .csv result output file.

Setup: Set Schrodinger Environment variable path

If the command $SCHRODINGER/run shows that the /run is a directory it means that the the SCHRODINGER environment variable path is not set. To set the environment variable path follow the below code:

export SCHRODINGER=installdir

The installdir is where the schrodinger is installed, mostly in /opt/schrodinger2023-1

Read more

Sometimes after restart the terminal the environment variable may lost, so to add the schrodinger environment permanently follow the steps:

  1. open bashrc by sudo nano .bashrc
  2. Then add the code at the bottom export SCHRODINGER="/opt/schrodinger2023-1"
  3. Reload the bashrc by source ~/.bashrc
  4. Now check the path was added or not by echo $SCHRODINGER, If the code returns /opt/schrodinger2023-1 that means the path added permanently.
  5. Now you may run $SCHRODINGER/run from anywhere of you machine