Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-09.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 63: No such file or directory. bzcat: Can't open input file 09: 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 63: No such file or directory. bzcat: Can't open input file 09: No such file or directory. nothing to compress du2.csh script updated ligand processing 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 0m3.827s user 0m0.612s sys 0m0.375s 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 0:1812 spheres. 207. 207. 207. 207. 208. 208. 208. 211. 214. 217. 217. 217. 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. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 225. 225. 225. 225. 225. 225. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 228. 228. 228. 228. 228. 228. 228. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 481. 482. 482. 484. 484. 484. 494. 495. 496. 496. 497. 497. 497. 497. 497. 497. 497. 499. 499. 499. 499. 499. 499. 499. 501. 501. 501. 501. 501. 501. 501. 501. 501. 501. 501. 501. 501. 511. 511. 511. 511. 511. 511. 511. 511. 511. 511. 511. 511. 511. 511. 511. 511. 511. 511. 511. 511. 512. 512. 512. 512. 512. 512. 512. 512. 512. 512. 512. 512. 516. 516. 516. 516. 516. 516. 516. 516. 516. 516. 516. 516. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 578. 825. 825. 834. 834. 834. 834. 834. 834. 835. 835. 836. 836. 844. 845. 845. 845.1003.1009.1009.1009.1009.1010.1010.1010.1010.1010.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1015.1015.1015.1021.1022.1022.1022.1022.1022.1022.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1024.1028.1028.1033.1040.1040.1040.1040.1040.1040.1040.1040.1040.1040.1040.1041.1041.1041.1041.1041.1049.1049.1050.1050.1050.1050.1051.1051.1051.1051.1051.1154.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1172.1172.1173.1173.1173.1173.1173.1691.1691.1703.1711.1712.1719.1719.1720.1720.1720.1720.1720.1720.1720.1720.1720.1720.1720.1720.1720.1720.1720.1720.1720.1720.1721.1721.1721.1721.1721.1721.1721.1721.1721.1731.1733.1733.1733.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1737.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1738.1742.1742.1742.1742.1744.1745.1745.1745.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1747.1747.1747.1747.1747.1747.1747.1747.1747.1748.1748.1748.1748.1749.1756.1756.1756.1756.1842.1842.1856.1859.1859.1867.1867.1867.1874.1879.1880.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1883.1883.1883.1883.1884.1894.1894.1894.1894.1896.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1906.1906.1906.1906.1906.1906.1906.1906.1906.1906.1907.1907.1907.1907.1907.1907.1907.1914.1914.1914.1914.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1917.1920.1920.1920.1920.1920.1920.1920.1920.1920.1922.1922.1922.1922.1923.1923.1923.1923.1923.1923.1923.1923.1923.1923.1923.1923.1923.1923.1923.1923.1924.1924.1948.1948.1948.1948.1948.1948.1948.1948.1948.1948.1949.1949.1949.1949.1952.1952.1952.1952.1952.1952.1952.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1960.1960.1960.1960.1960.1960.1960.1960.1960.1960.1960.1961.1961.1961.1961.1961.1961.1961.1961.1961.1961.1962.1962.1962.1962.1962.1962.1962.1982.1982.1982.1982.1985.1986.1987.1987.1987.1987.1987.1987.1987.1988.1988.1988.1988.1988.1988.1988.2000.2000.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2002.2002.2002.2002.2002.2002.2002.2002.2002.2002.2002.2002.2002.2002.2002.2009.2009.2009.2009.2009.2009.2009.2009.2009.2012.2012.2012.2012.2012.2012.2012.2012.2012.2012.2012.2012.2012.2012.2012.2012.2012.2012.2294.2294.2294.2296.2299.2299.2299.2299.2303.2303.2306.2306.2306.2306.2306.2306.2306.2306.2306.2309.2312.2312.2313.2314.2314.2314.2314.2314.2314.2314.2314.2350.2350.2350.2350.2350.2350.2350.2353.2353.2353.2353.2544.2544.2544.2544.2544.2544.2544.2544.2544.2544.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2546.2548.2548.2549.2549.2549.2549.2549.2549.2550.2550.2550.2550.2550.2550.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2552.2552.2552.2552.2553.2553.2553.2553.2553.2554.2554.2555.2555.2555.2555.2556.2556.2556.2556.2556.2556.2556.2556.2556.2556.2753.2753.2753.2753.2756.2756.2756.2756.2756.2756.2756.2756.2756.2756.2756.2756.2756.2756.2756.2756.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2771.2772.2772.2772.2772.2772.2772.2772.2772.2772.2772.2774.2776.2776.2776.2777.2777.2777.2777.2777.2777.2777.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2780.2780.2780.2780.2780.2780.2780.2780.2780.2780.2780.2781.2781.2781.2781.2781.2781.2781.2781.2781.2781.2781.2781.2781.2781.2781.2781.2781.2781.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2782.2783.2783.2783.2783.2787.2787.2787.2787.2787.2787.2787.2787.2787.2787.2787.2787.2787.2787.2787.2787.2787.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2788.2789.2792.2793.2793.2801.2801.2801.2801.2801.2801.2801.2806.2806.2806.2806.2806.2806.2806.2806.2806.2806.2806.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2807.2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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: 27 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. 27.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 * C3D* we had to cook * C2D* we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * C3C* we had to cook * C2C* we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * C3B* we had to cook * C2B* we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * C3A* we had to cook * C2A* we had to cook * C1A* we had to cook * NA * 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 * CMA* we had to cook * NB * we had to cook * CMB* we had to cook * CAB* we had to cook * CBB* we had to cook * NC * we had to cook * CMC* we had to cook * CAC* we had to cook * CBC* we had to cook * ND * we had to cook * CMD* 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* Creating DelPhi electrostatic grid real 0m29.131s user 0m25.280s sys 0m0.568s 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 * C3D* we had to cook * C2D* we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * C3C* we had to cook * C2C* we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * C3B* we had to cook * C2B* we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * C3A* we had to cook * C2A* we had to cook * C1A* we had to cook * NA * 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 * CMA* we had to cook * NB * we had to cook * CMB* we had to cook * CAB* we had to cook * CBB* we had to cook * NC * we had to cook * CMC* we had to cook * CAC* we had to cook * CBC* we had to cook * ND * we had to cook * CMD* 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* Creating DelPhi electrostatic grid real 0m30.192s user 0m24.858s sys 0m0.614s Creating box around spheres we were asked to cook * CHA* *CHA* 22 we had to cook * C4D* we had to cook * C3D* we had to cook * C2D* we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * C3C* we had to cook * C2C* we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * C3B* we had to cook * C2B* we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * C3A* we had to cook * C2A* we had to cook * C1A* we had to cook * NA * 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 * CMA* we had to cook * NB * we had to cook * CMB* we had to cook * CAB* we had to cook * CBB* we had to cook * NC * we had to cook * CMC* we had to cook * CAC* we had to cook * CBC* we had to cook * ND * we had to cook * CMD* 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* Creating chemgrid maps real 0m29.214s user 0m27.589s sys 0m0.304s Atomic solvent excluded volume calculations underway FORTRAN STOP real 23m55.614s user 23m54.581s sys 0m0.168s Checking for WARNINGS in OUTPARM. WARNING--parameters not found for ATOM 4667 FE HEM 819 sqrt(A), sqrt(B), and charge set to 0.0 -- WARNING--parameters not found for ATOM 4753 FE FE 3 sqrt(A), sqrt(B), and charge set to 0.0 Checking for WARNINGS in delphi.log. !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 !!! WARNING: HEM 819 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