[Step 1] First check if you have required environment setup in your .soft file. My .soft file looks like,
# This is the .soft file.
# It is used to customize your environment by setting up environment
# variables such as PATH and MANPATH.
# To learn what can be in this file, use 'man softenv'.
[Step 2] Create condor script including relevant arguments. I put all the required arguments in the "argument" command line of the script. I could get the result with using both batch system and system fork. Don't forget to transfer back the output file. My test script file is the following:
executable = /N/soft/linux-sles9-ppc64/amber9-ibm-64/exe/sander
arguments = -O -i amber_min.in -o min.out.$(Cluster) -c ZINC04273785_ini.crd
-p ZINC04273785_com.top -r ZINC04273785.crd
transfer_executable = false
should_transfer_files = yes
when_to_transfer_output = ON_EXIT
transfer_input_files = /home/leesangm/bio/mm_pbsa/amber_min.in,
universe = grid
grid_resource = gt2 gatekeeper.bigred.iu.teragrid.org/jobmanager-loadleveler
transfer_output_files = min.out.$(Cluster)
error = condorG.err.$(Cluster)
log = condorG.log.$(Cluster)
x509userproxy = /tmp/x509up_u500