Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-15.c.bkslab.org du2 starts 1 molecule processed, 0 errors convert.py (MDL SDF -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. mol2nam v1.9 Structure to Name Conversion OpenEye Scientific Software, February 2009 convert.py (Tripos MOL2 -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. mid: No such file or directory. hi: No such file or directory. lo: No such file or directory. mid: No such file or directory. first try already in then inzinc count is 0 bzcat: Can't open input file 48: No such file or directory. bzcat: Can't open input file 67: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. count is 0 nothing to compress bzcat: Can't open input file 48: No such file or directory. bzcat: Can't open input file 67: No such file or directory. nothing to compress du2.csh script updated ligand processing Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 147, in ? result = server.decoys(data) File "/usr/lib64/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib64/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib64/python2.4/xmlrpclib.py", line 1147, in request return self._parse_response(h.getfile(), sock) File "/usr/lib64/python2.4/xmlrpclib.py", line 1286, in _parse_response return u.close() File "/usr/lib64/python2.4/xmlrpclib.py", line 744, in close raise Fault(**self._stack[0]) xmlrpclib.Fault: MakeDOCK 2.0, modified by J.Irwin and M.Mysinger. Previous versions by D.M.Lorber, B.Q.Wei, A.N.Kirschner, and N.Huang Using scripts in /raid5/people/mysinger/xyz/dockenv. Creating binding-site residue list Creating molecular surface real 0m4.091s user 0m0.589s sys 0m0.521s Creating sphgen spheres Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 0:1818 spheres. 191. 195. 195. 198. 198. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 203. 203. 203. 203. 203. 203. 203. 203. 203. 203. 203. 203. 203. 203. 203. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 205. 206. 206. 206. 208. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 212. 212. 212. 212. 212. 212. 212. 212. 212. 215. 216. 216. 216. 216. 216. 216. 216. 216. 216. 216. 216. 216. 217. 218. 218. 218. 218. 218. 218. 218. 218. 218. 218. 218. 218. 218. 218. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 475. 476. 476. 476. 476. 489. 489. 489. 489. 490. 490. 490. 491. 491. 491. 491. 491. 491. 491. 491. 491. 491. 493. 493. 493. 495. 495. 495. 495. 495. 495. 495. 495. 495. 505. 506. 506. 510. 510. 510. 510. 510. 510. 510. 510. 510. 510. 510. 510. 510. 510. 510. 536. 536. 536. 537. 537. 537. 537. 537. 539. 539. 539. 539. 539. 539. 539. 539. 539. 539. 539. 539. 539. 539. 539. 539. 539. 539. 539. 539. 540. 540. 540. 540. 540. 540. 540. 540. 540. 540. 540. 572. 572. 572. 572. 572. 572. 572. 572. 572. 572. 572. 819. 819. 819. 828. 828. 828. 828. 828. 829. 829. 829. 829. 829. 829. 830. 830. 830. 830. 830. 830. 830. 830. 838. 838. 838. 839. 839. 839. 839. 840. 840. 997.1000.1000.1000.1000.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1004.1004.1004.1004.1004.1004.1004.1004.1004.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1009.1009.1009.1013.1014.1015.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1017.1017.1017.1017.1017.1017.1017.1017.1017.1017.1017.1017.1017.1017.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1027.1034.1034.1034.1034.1034.1034.1034.1034.1034.1034.1034.1034.1034.1034.1034.1034.1034.1034.1036.1039.1039.1039.1039.1041.1041.1041.1043.1044.1044.1045.1045.1045.1045.1148.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1162.1167.1167.1167.1167.1167.1167.1167.1167.1167.1167.1167.1167.1167.1167.1167.1167.1685.1685.1685.1685.1697.1702.1706.1706.1706.1706.1706.1706.1706.1706.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1713.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1714.1715.1715.1715.1715.1715.1715.1715.1715.1715.1721.1721.1725.1725.1727.1727.1727.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1731.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1736.1736.1737.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1740.1740.1740.1740.1740.1740.1740.1740.1740.1740.1740.1740.1741.1741.1741.1741.1741.1741.1741.1741.1741.1741.1741.1742.1742.1742.1742.1742.1742.1750.1750.1836.1836.1852.1852.1856.1857.1861.1876.1876.1876.1876.1876.1876.1876.1876.1876.1876.1876.1877.1878.1878.1883.1888.1888.1888.1888.1888.1888.1888.1888.1888.1888.1890.1890.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1900.1900.1900.1900.1900.1900.1900.1908.1909.1909.1909.1909.1909.1911.1911.1911.1914.1914.1914.1914.1914.1914.1914.1914.1914.1914.1915.1915.1915.1915.1915.1915.1915.1916.1917.1917.1917.1917.1917.1917.1917.1917.1917.1917.1917.1918.1942.1942.1942.1942.1942.1942.1942.1942.1942.1942.1942.1942.1943.1943.1943.1943.1943.1943.1946.1946.1946.1946.1946.1946.1946.1946.1946.1946.1946.1946.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1947.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1954.1954.1954.1954.1954.1954.1954.1954.1955.1955.1955.1955.1955.1955.1955.1955.1956.1956.1976.1976.1976.1976.1982.1982.1982.1982.1994.1994.1994.1994.1994.1994.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1996.1996.2003.2003.2003.2003.2003.2003.2003.2003.2003.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2281.2286.2286.2286.2286.2286.2286.2286.2290.2290.2293.2293.2293.2293.2293.2297.2297.2299.2299.2299.2299.2299.2301.2301.2301.2301.2301.2301.2301.2301.2301.2301.2301.2301.2301.2301.2301.2301.2301.2337.2337.2337.2337.2337.2337.2337.2337.2337.2339.2339.2340.2340.2531.2531.2531.2531.2531.2531.2531.2531.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2533.2535.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2537.2537.2537.2537.2537.2537.2538.2538.2538.2538.2538.2538.2539.2539.2539.2539.2539.2541.2541.2541.2543.2543.2543.2543.2543.2740.2740.2740.2740.2740.2740.2740.2740.2740.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2743.2744.2761.2762.2763.2763.2763.2763.2764.2764.2764.2764.2764.2764.2764.2764.2764.2764.2764.2764.2764.2764.2764.2764.2766.2766.2766.2766.2766.2766.2766.2766.2766.2766.2766.2766.2766.2767.2767.2767.2767.2767.2767.2767.2767.2767.2767.2767.2767.2768.2768.2768.2768.2768.2768.2768.2768.2768.2768.2768.2768.2769.2769.2769.2769.2769.2769.2769.2769.2769.2769.2769.2769.2769.2769.2769.2769.2769.2770.2770.2770.2772.2774.2774.2774.2774.2774.2774.2774.2774.2774.2774.2774.2774.2774.2774.2774.2774.2774.2774.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2780.2780.2780.2780.2780.2788.2788.2788.2788.2788.2788.2788.2788.2788.2793.2793.2793.2793.2793.2793.2793.2793.2793.2793.2793.2793.2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STOP Converting ligand atoms to spheres Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 26 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26.FORTRAN STOP Adding essential hydrogens to receptor Generating matching spheres for delphi Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 120 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.9046.9047.9048.9049.9050.9051.9052.9053.9054.9055.9056.9057.9058.9059.9060.9061.9062.9063.9064.9065.9066.9067.9068.9069.9070.9071.9072.9073.9074.9075.9076.9077.9078.9079.9080.9081.9082.9083.9084.9085.9086.9087.9088.9089.9090.9091.9092.9093.9094.9095.9096.9097.9098.9099.9100.9101.9102.9103.9104.9105.9106.9107.9108.9109.9110.9111.9112.9113.9114.9115.9116.9117.9118.9119.9120.FORTRAN STOP Generating faster matching2 spheres for docking Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 45 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.FORTRAN STOP Coloring matching spheres Generating slower matching3 spheres for docking Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 60 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.9046.9047.9048.9049.9050.9051.9052.9053.9054.9055.9056.9057.9058.9059.9060.FORTRAN STOP Coloring matching spheres Adding spheres to electrostatic grid we were asked to cook * CHA* *CHA* 22 we had to cook * C4D* we had to cook * ND * we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * NC * we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * NB * we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * NA * we had to cook * C1A* we had to cook * C2A* we had to cook * C3A* we had to cook * CMA* we had to cook * CAA* we had to cook * CBA* we had to cook * CGA* we had to cook * O2A* we had to cook * O1A* we had to cook * C2B* we had to cook * C3B* we had to cook * CAB* we had to cook * CBB* we had to cook * CMB* we had to cook * C2C* we had to cook * C3C* we had to cook * CAC* we had to cook * CBC* we had to cook * CMC* we had to cook * C2D* we had to cook * C3D* we had to cook * CAD* we had to cook * CBD* we had to cook * CGD* we had to cook * O2D* we had to cook * O1D* we had to cook * CMD* Creating DelPhi electrostatic grid real 0m25.124s user 0m22.191s sys 0m0.558s Adding spheres to tarted electrostatic grid we had to cook * NE2* we had to cook *HNE2* we had to cook *HNE1* we were asked to cook * CHA* *CHA* 22 we had to cook * C4D* we had to cook * ND * we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * NC * we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * NB * we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * NA * we had to cook * C1A* we had to cook * C2A* we had to cook * C3A* we had to cook * CMA* we had to cook * CAA* we had to cook * CBA* we had to cook * CGA* we had to cook * O2A* we had to cook * O1A* we had to cook * C2B* we had to cook * C3B* we had to cook * CAB* we had to cook * CBB* we had to cook * CMB* we had to cook * C2C* we had to cook * C3C* we had to cook * CAC* we had to cook * CBC* we had to cook * CMC* we had to cook * C2D* we had to cook * C3D* we had to cook * CAD* we had to cook * CBD* we had to cook * CGD* we had to cook * O2D* we had to cook * O1D* we had to cook * CMD* Creating DelPhi electrostatic grid real 0m26.783s user 0m22.590s sys 0m0.665s Creating box around spheres we were asked to cook * CHA* *CHA* 22 we had to cook * C4D* we had to cook * ND * we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * NC * we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * NB * we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * NA * we had to cook * C1A* we had to cook * C2A* we had to cook * C3A* we had to cook * CMA* we had to cook * CAA* we had to cook * CBA* we had to cook * CGA* we had to cook * O2A* we had to cook * O1A* we had to cook * C2B* we had to cook * C3B* we had to cook * CAB* we had to cook * CBB* we had to cook * CMB* we had to cook * C2C* we had to cook * C3C* we had to cook * CAC* we had to cook * CBC* we had to cook * CMC* we had to cook * C2D* we had to cook * C3D* we had to cook * CAD* we had to cook * CBD* we had to cook * CGD* we had to cook * O2D* we had to cook * O1D* we had to cook * CMD* Creating chemgrid maps real 0m25.343s user 0m23.086s sys 0m0.229s Atomic solvent excluded volume calculations underway FORTRAN STOP real 21m3.866s user 21m3.226s sys 0m0.144s Checking for WARNINGS in OUTPARM. WARNING--parameters not found for ATOM 4718 FE FE 2 sqrt(A), sqrt(B), and charge set to 0.0 WARNING--parameters not found for ATOM 4719 FE FE 3 sqrt(A), sqrt(B), and charge set to 0.0 Checking for WARNINGS in delphi.log. !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 End of MakeDOCK sphere and grid generation. Grid preparation completed normally. not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar failed to get similars