Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-07.c.bkslab.org du2 starts 1 molecule processed, 0 errors first try already in then inzinc count is 0 nothing to compress count is 0 nothing to compress nothing to compress 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 0m21.169s user 0m0.316s sys 0m0.136s 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 0:1297 spheres. 79. 81. 81. 82. 82. 82. 82. 84. 84. 84. 85. 85. 85. 85. 85. 86. 86. 86. 87. 87. 87. 87. 89. 89. 89. 89. 89. 89. 89. 89. 89. 90. 90. 90. 90. 90. 90. 90. 90. 90. 91. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 94. 94. 94. 94. 94. 94. 94. 103. 103. 103. 103. 103. 103. 103. 104. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 224. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 240. 240. 242. 242. 242. 242. 242. 242. 255. 255. 255. 255. 255. 256. 256. 256. 256. 256. 256. 256. 256. 256. 259. 259. 259. 259. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 267. 267. 268. 268. 268. 268. 268. 268. 268. 268. 268. 271. 271. 271. 271. 271. 271. 271. 271. 271. 272. 272. 272. 272. 272. 272. 275. 276. 276. 276. 276. 276. 277. 277. 277. 277. 279. 279. 279. 279. 279. 280. 280. 280. 280. 281. 281. 296. 296. 296. 296. 296. 296. 296. 296. 296. 296. 296. 303. 303. 303. 303. 303. 303. 303. 303. 420. 423. 426. 426. 430. 430. 430. 430. 430. 430. 431. 431. 431. 431. 431. 434. 434. 435. 435. 435. 435. 435. 435. 435. 436. 436. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 439. 439. 439. 439. 439. 439. 439. 439. 439. 440. 447. 447. 447. 448. 448. 448. 448. 448. 448. 448. 451. 451. 451. 452. 452. 452. 452. 452. 452. 452. 452. 452. 452. 452. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 454. 454. 454. 454. 454. 454. 454. 455. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 457. 457. 458. 458. 458. 459. 459. 460. 464. 464. 465. 467. 467. 467. 467. 467. 467. 467. 468. 468. 468. 468. 470. 470. 470. 470. 472. 472. 475. 478. 481. 482. 482. 482. 482. 482. 483. 483. 483. 483. 483. 483. 483. 483. 483. 483. 483. 484. 486. 486. 486. 486. 486. 486. 487. 487. 487. 487. 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. 488. 488. 488. 488. 488. 488. 488. 488. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 490. 493. 497. 541. 541. 541. 544. 544. 544. 544. 544. 544. 544. 544. 545. 545. 545. 545. 545. 548. 548. 549. 549. 549. 549. 549. 549. 728. 728. 728. 728. 730. 730. 730. 730. 730. 730. 730. 730. 730. 731. 731. 737. 737. 737. 737. 746. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 754. 754. 754. 755. 755. 755. 755. 755. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 764. 764. 764. 764. 764. 764. 764. 764. 764. 764. 764. 764. 764. 764. 764. 765. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 794. 794. 794. 794. 800. 800. 801. 801. 801. 801. 802. 802. 806. 806. 806. 806. 806. 806. 808. 808. 808. 808. 808. 808. 808. 810. 810. 810. 810. 810. 810. 810. 813. 813. 813. 813. 816. 819. 819. 819. 827. 827. 827. 827. 827. 827. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 999. 999.1000.1002.1002.1002.1002.1002.1002.1002.1002.1002.1004.1004.1005.1005.1005.1005.1005.1005.1005.1007.1007.1007.1007.1007.1007.1007.1007.1008.1008.1008.1008.1009.1009.1009.1009.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1011.1011.1011.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1014.1023.1023.1023.1023.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1144.1144.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1175.1176.1176.1176.1176.1179.1179.1179.1179.1179.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1187.1188.1188.1188.1189.1189.1189.1189.1189.1189.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1192.1192.1192.1192.1192.1197.1197.1197.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1199.1199.1199.1199.1199.1199.1200.1200.1200.1200.1200.1200.1200.1200.1200.1201.1201.1201.1201.1209.1209.1209.1217.1217.1217.1230.1230.1230.1230.1236.1236.1341.1346.1346.1346.1346.1349.1349.1349.1349.1349.1350.1350.1350.1350.1350.1350.1350.1359.1365.1365.1365.1368.1368.1368.1368.1368.1368.1368.1368.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1374.1374.1374.1374.1374.1374.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1385.1385.1385.1385.1385.1385.1385.1386.1386.1386.1386.1387.1387.1387.1387.1387.1387.1388.1390.1390.1391.1392.1392.1392.1392.1392.1392.1392.1392.1392.1393.1393.1395.1395.1395.1395.1396.1402.1402.1402.1403.1403.1405.1407.1407.1408.1408.1408.1409.1412.1413.1413.1413.1417.1630.1630.1630.1630.1630.1630.1630.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1650.1650.1650.1651.1651.1651.1651.1651.1651.1651.1651.1652.1652.1664.1664.1666.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1669.1669.1674.1674.1674.1674.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1696.1696.1696.1696.1696.1696.1696.1696.1696.1696.1696.1696.1696.1696.1696.1714.1714.1720.1720.1720.1721.1721.1726.1726.1726.1726.1726.1728.1728.1728.1730.1730.1730.1730.1730.1730.1730.1732.1732.1733.1733.1733.1734.1734.1734.1734.1736.1736.1736.1736.1739.1739.1747.1747.1756.1756.1756.1756.1756.1756.1756.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: 54 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. 41. 42. 43. 44. 45. 46. 47. 48. 49. 50. 51. 52. 53. 54.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 1m40.324s user 0m23.030s sys 0m0.648s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m45.323s user 0m24.346s sys 0m0.601s Creating box around spheres Creating chemgrid maps real 0m38.304s user 0m14.975s sys 0m0.176s Atomic solvent excluded volume calculations underway FORTRAN STOP real 87m23.770s user 29m16.228s sys 0m0.254s 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.