Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-05.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 41: No such file or directory. bzcat: Can't open input file 21: 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 41: No such file or directory. bzcat: Can't open input file 48: 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 41: No such file or directory. bzcat: Can't open input file 21: No such file or directory. bzcat: Can't open input file 41: No such file or directory. bzcat: Can't open input file 48: 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 0m31.607s user 0m0.267s sys 0m0.079s 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 0:1639 spheres. 63. 66. 66. 66. 66. 66. 66. 68. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 70. 70. 70. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 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. 75. 75. 75. 75. 75. 75. 76. 84. 84. 84. 84. 84. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 172. 182. 182. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 216. 219. 220. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 228. 229. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 231. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 255. 258. 258. 258. 260. 260. 261. 261. 261. 261. 348. 349. 352. 352. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 357. 358. 358. 358. 358. 358. 359. 359. 359. 361. 361. 361. 361. 362. 362. 362. 362. 362. 364. 364. 364. 367. 367. 367. 367. 367. 367. 367. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 371. 371. 372. 372. 372. 372. 372. 372. 372. 372. 373. 373. 373. 373. 373. 373. 373. 373. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 376. 376. 376. 376. 376. 376. 376. 376. 376. 377. 377. 378. 379. 380. 382. 383. 383. 383. 383. 383. 383. 383. 385. 385. 385. 385. 385. 385. 385. 385. 385. 386. 386. 386. 386. 386. 386. 386. 386. 386. 389. 389. 390. 390. 390. 390. 390. 390. 390. 390. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 393. 397. 397. 397. 397. 398. 398. 398. 398. 398. 398. 398. 398. 400. 400. 401. 401. 401. 401. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 407. 407. 408. 412. 414. 414. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 419. 419. 419. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 425. 425. 425. 426. 426. 426. 426. 426. 426. 426. 426. 426. 562. 566. 566. 566. 566. 566. 566. 566. 566. 566. 566. 566. 566. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 575. 575. 575. 575. 575. 575. 575. 597. 597. 598. 598. 598. 598. 598. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 600. 600. 600. 600. 600. 600. 600. 605. 607. 610. 612. 612. 612. 612. 612. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 620. 620. 620. 620. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 622. 622. 622. 622. 622. 622. 622. 622. 622. 622. 622. 622. 630. 630. 630. 630. 630. 630. 630. 630. 630. 630. 635. 636. 636. 637. 637. 637. 637. 637. 637. 637. 637. 637. 637. 637. 637. 644. 644. 644. 644. 644. 652. 658. 658. 658. 658. 659. 659. 659. 659. 659. 659. 659. 659. 662. 662. 662. 662. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 666. 668. 668. 668. 668. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 822. 822. 822. 822. 822. 822. 823. 824. 824. 824. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 828. 828. 828. 828. 828. 828. 829. 829. 837. 837. 837. 838. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 925. 934. 935. 935. 935. 943. 943. 943. 943. 943. 943. 943. 943. 943. 943. 944. 944. 944. 944. 952. 952. 952. 952. 952. 952. 952. 952. 952. 952. 962. 962. 962. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 965. 965. 965. 965. 965. 965. 965. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 969. 972. 973. 973. 973. 973. 974. 974. 974. 974. 974. 974. 974. 974. 975. 975. 975. 975. 976. 976. 976. 976. 976. 976. 976. 976. 976. 976. 976. 981. 981. 981. 981. 981. 981. 982. 982. 983. 983. 983. 983. 983. 983. 983. 983. 983. 983. 983. 983. 984. 984. 984. 984. 984. 991. 991. 991. 991. 991. 991. 991. 997. 997. 997. 997. 997. 997.1005.1005.1005.1005.1106.1106.1106.1106.1107.1107.1107.1107.1107.1107.1107.1110.1110.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1113.1113.1113.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1117.1117.1117.1117.1120.1120.1120.1120.1120.1122.1122.1123.1123.1123.1123.1123.1123.1124.1124.1124.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1128.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1131.1131.1131.1131.1131.1133.1133.1133.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1138.1139.1139.1140.1141.1141.1142.1142.1142.1142.1142.1143.1143.1143.1143.1144.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1150.1150.1150.1151.1151.1151.1151.1151.1151.1151.1151.1154.1154.1154.1154.1154.1154.1155.1155.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1161.1161.1161.1161.1164.1165.1165.1165.1165.1165.1165.1177.1179.1179.1179.1334.1334.1334.1334.1334.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1349.1351.1351.1351.1351.1351.1351.1351.1351.1351.1352.1352.1352.1352.1352.1352.1352.1358.1358.1358.1360.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1368.1368.1368.1368.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1374.1374.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1379.1381.1383.1383.1383.1388.1390.1390.1390.1390.1390.1390.1390.1398.1398.1398.1398.1405.1405.1405.1410.1410.1411.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1413.1415.1415.1415.1415.1415.1415.1418.1418.1418.1418.1418.1418.1418.1418.1419.1419.1419.1419.1419.1419.1419.1419.1419.1421.1421.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: 51 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.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 1m28.705s user 0m20.837s sys 0m0.462s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m34.201s user 0m21.773s sys 0m0.508s Creating box around spheres Creating chemgrid maps real 0m44.354s user 0m13.062s sys 0m0.216s Atomic solvent excluded volume calculations underway FORTRAN STOP real 71m2.672s user 26m55.004s sys 0m0.201s 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.