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job.xml
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job.xml
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<job_desc>
<task>
<application>unzip</application>
<command_line> -qq -o "*.zip" -d "."</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>grompp.exe</application>
<command_line>-f em.mdp -c ligand_GMX.gro -p ligand_GMX.top</command_line>
<weight>1</weight>
</task>
<task>
<application>mdrun.exe</application>
<command_line>-v -s topol.tpr -c ligand.pdb</command_line>
<weight>1</weight>
<fraction_done_filename>progress.txt</fraction_done_filename>
</task>
<task>
<application>./Python25/python.exe</application>
<command_line>"./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py" -l ligand.pdb -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=1 -p ga_num_evals=2500 -p seed=946973</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_1.dlg</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/write_largest_cluster_ligand.py" -v</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/pdbqt_to_pdb.py" -f ligand_BC.pdbqt -o minenergy.pdb</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=1 -p ga_num_evals=2500 -p seed=593050</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_2.dlg</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/write_largest_cluster_ligand.py" -v</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/pdbqt_to_pdb.py" -f ligand_BC.pdbqt -o minenergy.pdb</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=1 -p ga_num_evals=2500 -p seed=82529</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_3.dlg</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/write_largest_cluster_ligand.py" -v</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/pdbqt_to_pdb.py" -f ligand_BC.pdbqt -o minenergy.pdb</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=1 -p ga_num_evals=2500 -p seed=28460</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_4.dlg</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/write_largest_cluster_ligand.py" -v</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/pdbqt_to_pdb.py" -f ligand_BC.pdbqt -o minenergy.pdb</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=1 -p ga_num_evals=2500 -p seed=16485</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_5.dlg</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/write_largest_cluster_ligand.py" -v</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/pdbqt_to_pdb.py" -f ligand_BC.pdbqt -o minenergy.pdb</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=1 -p ga_num_evals=2500 -p seed=315154</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_6.dlg</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/write_largest_cluster_ligand.py" -v</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/pdbqt_to_pdb.py" -f ligand_BC.pdbqt -o minenergy.pdb</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=1 -p ga_num_evals=2500 -p seed=400039</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_7.dlg</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/write_largest_cluster_ligand.py" -v</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/pdbqt_to_pdb.py" -f ligand_BC.pdbqt -o minenergy.pdb</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=1 -p ga_num_evals=2500 -p seed=178951</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_8.dlg</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/write_largest_cluster_ligand.py" -v</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/pdbqt_to_pdb.py" -f ligand_BC.pdbqt -o minenergy.pdb</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=1 -p ga_num_evals=2500 -p seed=509876</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_9.dlg</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/write_largest_cluster_ligand.py" -v</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/pdbqt_to_pdb.py" -f ligand_BC.pdbqt -o minenergy.pdb</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=1 -p ga_num_evals=2500 -p seed=409032</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_10.dlg</command_line>
<weight>1</weight>
</task>
<task>
<application>7za.exe</application>
<stdout_filename>stdout</stdout_filename>
<stderr_filename>stderr</stderr_filename>
<command_line> a out.7z *.dlg out.glg receptor.gpf ligand_receptor.dpf job.xml ligand.pdb</command_line>
<weight>1</weight>
</task>
</job_desc>