Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-14.c.bkslab.org du2 starts 1 molecule processed, 0 errors first try already in then inzinc count is 0 bzcat: Can't open input file 32: No such file or directory. bzcat: Can't open input file 71: 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 32: No such file or directory. bzcat: Can't open input file 71: 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 2m21.180s user 0m0.319s sys 0m0.135s 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 0:1194 spheres. 79. 79. 79. 79. 79. 79. 81. 81. 81. 84. 84. 84. 84. 84. 84. 84. 84. 84. 85. 85. 87. 87. 87. 90. 90. 90. 90. 90. 91. 91. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 94. 94. 94. 94. 94. 94. 103. 103. 103. 103. 103. 103. 106. 106. 106. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 230. 230. 230. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 240. 242. 242. 242. 242. 248. 248. 248. 248. 248. 248. 248. 248. 250. 250. 252. 252. 252. 255. 255. 255. 255. 255. 256. 256. 256. 256. 259. 259. 259. 259. 259. 259. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 267. 268. 268. 268. 268. 268. 268. 268. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 272. 272. 272. 272. 272. 272. 274. 277. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 289. 297. 297. 297. 297. 420. 429. 429. 430. 430. 430. 430. 431. 431. 431. 431. 431. 431. 431. 431. 435. 437. 437. 437. 437. 438. 438. 438. 438. 438. 438. 438. 439. 442. 447. 448. 448. 448. 448. 448. 448. 448. 448. 451. 451. 451. 451. 451. 451. 451. 451. 451. 452. 452. 452. 452. 452. 452. 452. 452. 452. 452. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 454. 454. 454. 454. 454. 454. 454. 454. 454. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 457. 457. 457. 457. 457. 457. 457. 457. 458. 458. 464. 464. 464. 464. 465. 465. 467. 467. 467. 467. 470. 470. 470. 470. 470. 470. 470. 470. 470. 470. 470. 470. 472. 472. 473. 473. 475. 475. 478. 478. 478. 482. 482. 483. 483. 483. 483. 485. 485. 485. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 488. 488. 488. 488. 488. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 497. 497. 497. 685. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 704. 704. 704. 704. 704. 704. 723. 723. 723. 723. 723. 724. 724. 724. 725. 739. 739. 739. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 742. 747. 747. 747. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 756. 756. 756. 756. 757. 757. 757. 757. 757. 759. 759. 760. 760. 769. 769. 769. 769. 777. 777. 777. 777. 787. 787. 787. 787. 787. 787. 787. 787. 787. 793. 793. 793. 793. 795. 795. 795. 795. 797. 800. 800. 800. 800. 800. 800. 800. 800. 801. 801. 802. 803. 803. 803. 803. 803. 803. 806. 806. 806. 806. 806. 806. 806. 807. 807. 807. 807. 809. 809. 809. 812. 815. 815. 815. 815. 815. 815. 815. 815. 828. 829. 829. 829. 829. 992. 995. 995.1002.1002.1002.1002.1002.1002.1002.1003.1003.1003.1004.1004.1004.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1007.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1016.1016.1016.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1137.1137.1137.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1153.1153.1154.1154.1155.1155.1155.1155.1155.1155.1155.1168.1169.1169.1169.1169.1169.1169.1169.1169.1169.1172.1172.1172.1172.1172.1172.1172.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1181.1182.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1185.1185.1185.1185.1190.1190.1190.1190.1190.1191.1191.1191.1192.1192.1192.1192.1192.1192.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1201.1201.1201.1202.1210.1210.1210.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1333.1333.1333.1334.1334.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1341.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1348.1348.1351.1352.1352.1358.1358.1358.1358.1358.1358.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1364.1364.1364.1364.1365.1365.1365.1365.1365.1365.1365.1365.1365.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1367.1367.1367.1367.1367.1367.1367.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1378.1380.1380.1380.1380.1380.1381.1383.1384.1384.1384.1385.1385.1385.1385.1385.1385.1385.1385.1385.1386.1386.1388.1388.1388.1388.1388.1388.1388.1388.1395.1395.1395.1398.1400.1400.1400.1400.1400.1400.1400.1400.1400.1401.1405.1406.1406.1597.1598.1598.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1602.1602.1602.1602.1602.1602.1602.1602.1602.1602.1618.1618.1618.1634.1634.1634.1634.1635.1637.1637.1637.1637.1637.1637.1637.1637.1643.1643.1647.1652.1652.1652.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1655.1655.1655.1655.1655.1660.1660.1661.1661.1661.1661.1661.1661.1662.1662.1662.1672.1672.1672.1672.1672.1672.1674.1680.1680.1681.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1691.1691.1691.1691.1691.1691.1700.1700.1700.1706.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1714.1714.1714.1716.1716.1716.1716.1716.1719.1719.1719.1719.1720.1720.1720.1722.1722.1725.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: 40 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. 40.FORTRAN STOP Adding essential hydrogens to receptor #@jens_hydrogens.csh rec.pdb 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 1m49.266s user 0m22.050s sys 0m0.615s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m34.415s user 0m21.366s sys 0m0.481s Creating box around spheres Creating chemgrid maps real 0m46.442s user 0m13.905s sys 0m0.158s Atomic solvent excluded volume calculations underway FORTRAN STOP real 83m48.617s user 28m5.174s sys 0m0.166s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. Stop before docking.