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job_.xml
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<job_desc>
<task>
<application>unzip</application>
<command_line> -qq -o "./MGLTools*.zip" -d "."</command_line>
<weight>1</weight>
</task>
<task>
<application>7za.exe</application>
<command_line> e ligand.mol2.7z</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<command_line>make_sitecustomize.py "."</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<command_line>"./MGLToolsPckgs/Support/sitecustomize.py"</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<command_line>"./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py" -l ligand.mol2 -o ligand.pdbqt</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<command_line>"./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py" -U nphs_lps_waters -r receptor.pdb -o receptor.pdbqt</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<stdout_filename>stdout</stdout_filename>
<stderr_filename>stderr</stderr_filename>
<command_line>"./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py" -l ligand.pdbqt -r receptor.pdbqt -p custom_parameter_file=1 -p parameter_file=AD4_parameters.dat</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<stdout_filename>stdout</stdout_filename>
<stderr_filename>stderr</stderr_filename>
<command_line>"./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py" -l ligand.pdbqt -r receptor.pdbqt -p compute_unbound_extended_flag=0 -p ga_run=</command_line>
<weight>1</weight>
</task>
<task>
<application>autogrid</application>
<stdout_filename>stdout</stdout_filename>
<stderr_filename>stderr</stderr_filename>
<command_line> -p receptor.gpf -l out.glg </command_line>
<weight>1</weight>
</task>
<task>
<application>autodock</application>
<stdout_filename>stdout</stdout_filename>
<stderr_filename>stderr</stderr_filename>
<command_line> -p ligand_receptor.dpf -l out.dlg</command_line>
<weight>0</weight>
<fraction_done_filename>progress.txt</fraction_done_filename>
</task>
<task>
<application>7za.exe</application>
<stdout_filename>stdout</stdout_filename>
<stderr_filename>stderr</stderr_filename>
<command_line> a out.7z out.dlg out.glg receptor.gpf ligand_receptor.dpf job.xml</command_line>
<weight>1</weight>
</task>
</job_desc>
<job_desc>
<task>
<application>unzip</application>
<command_line> -qq -o "./MGLTools*.zip" -d "."</command_line>
<weight>1</weight>
</task>
<task>
<application>7za.exe</application>
<command_line> e ligand.mol2.7z</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<command_line>make_sitecustomize.py "."</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<command_line>"./MGLToolsPckgs/Support/sitecustomize.py"</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<command_line>"./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py" -l ligand.mol2 -o ligand.pdbqt</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<command_line>"./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py" -U nphs_lps_waters -r receptor.pdb -o receptor.pdbqt</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<stdout_filename>stdout</stdout_filename>
<stderr_filename>stderr</stderr_filename>
<command_line>"./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py" -l ligand.pdbqt -r receptor.pdbqt -p custom_parameter_file=1 -p parameter_file=AD4_parameters.dat</command_line>
<weight>1</weight>
</task>
<task>
<application>./Python25/python.exe</application>
<stdout_filename>stdout</stdout_filename>
<stderr_filename>stderr</stderr_filename>
<command_line>"./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py" -l ligand.pdbqt -r receptor.pdbqt -p compute_unbound_extended_flag=0 -p ga_run=</command_line>
<weight>1</weight>
</task>
<task>
<application>autogrid</application>
<stdout_filename>stdout</stdout_filename>
<stderr_filename>stderr</stderr_filename>
<command_line> -p receptor.gpf -l out.glg </command_line>
<weight>1</weight>
</task>
<task>
<application>autodock</application>
<stdout_filename>stdout</stdout_filename>
<stderr_filename>stderr</stderr_filename>
<command_line> -p ligand_receptor.dpf -l out.dlg</command_line>
<weight>0</weight>
<fraction_done_filename>progress.txt</fraction_done_filename>
</task>
<task>
<application>7za.exe</application>
<stdout_filename>stdout</stdout_filename>
<stderr_filename>stderr</stderr_filename>
<command_line> a out.7z out.dlg out.glg receptor.gpf ligand_receptor.dpf job.xml</command_line>
<weight>1</weight>
</task>
</job_desc>