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 42: No such file or directory. bzcat: Can't open input file 17: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. count is 0 bzcat: Can't open input file 43: No such file or directory. bzcat: Can't open input file 68: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. bzcat: Can't open input file 42: No such file or directory. bzcat: Can't open input file 17: No such file or directory. bzcat: Can't open input file 43: No such file or directory. bzcat: Can't open input file 68: No such file or directory. 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 0m23.454s user 0m0.257s sys 0m0.113s 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 0:1363 spheres. 66. 66. 66. 66. 66. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 75. 75. 75. 84. 84. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 183. 183. 191. 191. 191. 191. 191. 197. 197. 197. 199. 199. 199. 199. 199. 199. 199. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 219. 220. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 228. 228. 228. 228. 228. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 347. 347. 347. 347. 347. 347. 351. 352. 352. 352. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 358. 359. 359. 359. 359. 359. 361. 361. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 364. 365. 365. 365. 365. 365. 365. 365. 365. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 370. 370. 373. 374. 375. 375. 375. 375. 375. 375. 375. 376. 377. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 379. 379. 379. 379. 380. 380. 380. 380. 380. 380. 381. 381. 381. 381. 381. 381. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 384. 384. 384. 384. 388. 391. 391. 391. 391. 391. 391. 391. 391. 391. 391. 391. 391. 393. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 396. 396. 396. 396. 396. 396. 396. 396. 396. 396. 396. 397. 397. 397. 397. 397. 397. 397. 399. 399. 399. 399. 399. 404. 416. 416. 416. 562. 563. 563. 563. 563. 563. 592. 594. 594. 594. 594. 594. 595. 595. 595. 595. 595. 595. 596. 596. 596. 596. 596. 596. 597. 601. 604. 607. 608. 608. 608. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 611. 611. 611. 613. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 619. 619. 619. 619. 619. 619. 619. 619. 620. 625. 625. 625. 625. 625. 626. 627. 627. 627. 627. 627. 630. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 650. 650. 650. 656. 656. 656. 657. 657. 657. 657. 657. 657. 657. 657. 657. 657. 657. 657. 660. 660. 660. 660. 660. 660. 660. 662. 663. 663. 663. 663. 663. 663. 663. 663. 663. 666. 666. 817. 817. 817. 817. 818. 818. 818. 819. 819. 819. 819. 820. 820. 820. 820. 822. 822. 822. 822. 822. 822. 822. 822. 822. 823. 823. 823. 823. 823. 823. 823. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 826. 826. 826. 826. 826. 826. 826. 826. 835. 835. 835. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 948. 950. 950. 950. 950. 950. 950. 950. 950. 950. 950. 950. 950. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 963. 963. 963. 963. 963. 963. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 967. 970. 970. 971. 971. 971. 971. 971. 972. 972. 972. 972. 972. 972. 972. 972. 973. 973. 973. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 978. 979. 979. 979. 979. 979. 979. 979. 980. 980. 981. 981. 981. 981. 981. 982. 982. 982. 982. 987. 987. 987. 987. 987. 987. 987. 987. 987. 994. 994. 994. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996. 996.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1097.1097.1097.1097.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1102.1105.1105.1106.1111.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1120.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1133.1133.1133.1133.1133.1134.1135.1135.1135.1135.1137.1137.1137.1139.1139.1139.1139.1140.1141.1141.1145.1145.1146.1146.1146.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1148.1148.1148.1148.1148.1148.1148.1148.1148.1150.1153.1153.1153.1154.1154.1154.1154.1154.1154.1154.1154.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1167.1343.1343.1343.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1346.1346.1346.1346.1346.1346.1346.1346.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1348.1348.1348.1348.1348.1348.1348.1348.1348.1348.1348.1348.1359.1359.1359.1359.1359.1359.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1362.1362.1362.1362.1362.1364.1367.1367.1367.1367.1367.1368.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1378.1378.1385.1385.1386.1386.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1407.1407.1407.1408.1408.1408.1408.1408.1408.1409.1411.1411.1411.1413.1413.1414.1414.1414.1414.1414.1414.1414.1414.1417.1417.1417.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: 38 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.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 1m27.335s user 0m20.679s sys 0m0.513s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m37.108s user 0m20.531s sys 0m0.537s Creating box around spheres Creating chemgrid maps real 0m53.224s user 0m14.666s sys 0m0.209s Atomic solvent excluded volume calculations underway FORTRAN STOP real 80m20.721s user 26m13.910s sys 0m0.137s 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.