Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-1-20.c.bkslab.org du2 starts 1 molecule processed, 0 errors convert.py (MDL SDF -> Isomeric SMILES): mols in: 2 mols out: 2 Total: 2 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 93: No such file or directory. bzcat: Can't open input file 80: 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 93: No such file or directory. bzcat: Can't open input file 80: 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 0m5.019s user 0m0.831s sys 0m0.690s 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 0:1408 spheres. 299. 299. 299. 299. 299. 299. 299. 299. 299. 310. 310. 310. 310. 313. 313. 314. 314. 314. 314. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 316. 318. 318. 318. 318. 318. 318. 318. 318. 318. 318. 318. 318. 318. 318. 318. 319. 322. 322. 322. 323. 323. 323. 323. 323. 323. 323. 324. 324. 324. 324. 324. 324. 324. 325. 329. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 331. 331. 331. 331. 331. 331. 332. 332. 332. 333. 333. 333. 333. 333. 333. 333. 333. 336. 336. 337. 338. 339. 339. 339. 340. 340. 340. 340. 340. 340. 340. 340. 340. 340. 341. 341. 341. 342. 342. 342. 342. 342. 342. 342. 342. 342. 342. 342. 342. 342. 342. 346. 348. 348. 348. 348. 348. 348. 348. 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742.1194.1194.1194.1194.1194.1194.1200.1200.1200.1200.1200.1200.1201.1201.1201.1201.1201.1201.1201.1201.1417.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1422.1422.1422.1423.1423.1423.1424.1424.1424.1424.1424.1424.1424.1424.1424.1424.1424.1424.1424.1425.1425.1429.1429.1430.1430.1431.1431.1441.1441.1747.1747.1747.1747.1747.1747.1747.1747.1747.1747.1747.1747.1748.1748.1748.1748.1748.1751.1751.1751.1753.1753.1753.1753.1753.1753.1753.1753.1753.1753.1753.1753.1753.1753.1753.1753.1753.1753.1753.1755.1756.1756.1756.1756.1756.1756.1756.1756.1756.1756.1756.1756.1756.1756.1756.1756.1756.1756.1756.1757.1757.1763.1763.1769.1769.1769.1769.1769.1769.1769.1769.1769.1769.1769.1769.1769.1772.1772.1772.1772.1772.1772.1772.1772.1772.1772.1772.1772.1772.1772.1773.1777.1778.1778.1778.1778.1778.1778.1778.1778.1778.1778.1778.1778.1778.1778.1778.1779.1780.1780.1780.1780.1780.1781.1783.1783.1784.1784.1784.1784.1784.1784.1784.1785.1785.1785.1785.1786.1786.1786.1786.1786.1786.1786.1786.1786.1786.1786.1786.1787.1787.1787.1787.1787.1787.1787.1789.1789.1789.1790.1791.1791.1791.1791.1791.1791.1791.1791.1791.1791.1792.1792.1794.1794.1794.1794.1794.1794.1794.1794.1794.1794.1794.1794.1794.1795.1795.1795.1795.1806.1806.1806.1806.1806.1807.1807.1809.1809.1809.1809.1809.1809.1809.1809.1809.1809.1809.1809.1809.1809.1809.1809.1818.1820.1820.1820.1821.1822.1822.1822.1822.1822.1822.1822.1822.1824.1825.1825.1825.1825.1825.1825.1825.1825.1825.1825.1825.1825.1825.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1827.1830.1830.1830.1830.1830.1832.1832.1832.1832.1832.1832.1832.1832.1832.1832.1832.1832.1833.1833.1833.1834.1834.1834.1834.1834.1834.1834.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1836.1836.1836.1836.1837.1837.1839.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1841.1842.1842.1842.1842.1844.1844.1844.1844.1845.1848.1848.1848.1848.1848.1848.1848.1848.1848.1849.1849.1849.1849.1849.1849.1849.1849.1849.1849.1849.1850.1850.1850.1850.1850.1850.1851.1851.1851.1859.1863.1865.1865.1865.1865.1866.1866.1866.1867.1867.1867.1868.1868.1868.1868.1868.1868.1868.1868.1868.1869.1869.1869.1869.1869.1869.1869.1869.1871.1871.1876.1876.1876.1876.1876.1876.1881.1881.1881.1881.1881.1881.1883.1887.1887.1887.1887.1887.1887.1887.1887.1887.1887.1887.1887.1887.1887.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1904.1907.1907.1907.1907.2181.2183.2183.2183.2183.2184.2184.2184.2185.2185.2185.2185.2185.2185.2185.2186.2186.2186.2186.2186.2186.2186.2186.2186.2187.2187.2187.2187.2187.2187.2187.2188.2188.2188.2188.2193.2196.2196.2196.2196.2196.2196.2196.2196.2196.2196.2196.2196.2196.2196.2196.2196.2196.2196.2196.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2198.2199.2199.2199.2199.2199.2199.2199.2199.2199.2199.2207.2207.2207.2207.2207.2207.2211.2211.2211.2211.2211.2211.2211.2214.2217.2217.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2220.2220.2220.2220.2220.2220.2220.2220.2220.2220.2220.2220.2220.2220.2220.2220.2220.2220.2220.2221.2221.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2223.2225.2225.2225.2225.2225.2225.2225.2225.2225.2227.2229.2229.2229.2229.2230.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2231.2235.2235.2236.2236.2681.2990.2990.2990.2990.2990.2990.2990.2990.2990.2996.2996.2998.3001.3005.3005.3005.3005.3005.3005.3005.3005.3005.3005.3005.3009.3011.3011.3015.3016.3016.3016.3016.3016.3016.3016.3016.3021.3021.3021.3021.3021.3021.3021.3028.3028.3047.3047.3047.3047.3048.3048.3049.3049.3049.3049.3049.3049.3049.3049.3049.3049.FORTRAN 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: 39 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. 28. 29. 30. 31. 32. 33. 34. 35. 36. 37. 38. 39.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 Creating DelPhi electrostatic grid real 0m34.564s user 0m32.519s sys 0m0.981s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m34.837s user 0m32.605s sys 0m1.013s Creating box around spheres Creating chemgrid maps real 1m9.307s user 1m8.385s sys 0m0.358s Atomic solvent excluded volume calculations underway FORTRAN STOP real 24m5.994s user 24m4.358s sys 0m0.082s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. File name = ../grids/distmap In source file scoreopt_so.f, at line number 625 PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. File name = ../grids/distmap In source file scoreopt_so.f, at line number 625 PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. 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