Good News! There were AMBER installations in three of SDSC machines: DataStar, BlueGene and Teragrid. For the serial example, I could not run on BlueGene, because there was no "sander" executable under amber9 installation. However, here are some guidelines about running amber on SDSC machines.
All of the machines keep the amber installation under the directory with same name structure.
Therefore, just set the environment and run the same command on each of the account.
leesangm/amber> setenv AMBERHOME /usr/local/apps/amber9
leesangm/amber> set path = ( $path $AMBERHOME/exe )
leesangm/amber> $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