Step 1. Setup the environment in .soft file
Step 2. Go to the work directory and run the following command
$AMBERHOME/exe/sander -O -i amber_min.in -o min.out -c ZINC04273785_ini.crd -p ZINC04273785_com.top -r ZINC04273785.crd -ref ZINC04273785_ini.crd
Step 3. Output file is updated every 2 minutes and it took 20 minutes for me to finish the job completely.