Thursday, March 6, 2008

Running AMBER-pbsa on BigRed:[1] Serial-Interactive

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 -o min.out -c ZINC04273785_ini.crd -p -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.

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