Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-12.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 59: No such file or directory. bzcat: Can't open input file 50: 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 59: No such file or directory. bzcat: Can't open input file 50: 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 0m34.639s user 0m0.270s sys 0m0.083s 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 0:1290 spheres. 66. 68. 68. 68. 68. 69. 69. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 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. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 84. 84. 84. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 183. 183. 183. 183. 183. 183. 183. 183. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 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. 219. 219. 220. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 227. 228. 228. 228. 228. 228. 229. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 245. 245. 245. 245. 245. 245. 245. 255. 255. 255. 255. 256. 256. 256. 256. 258. 258. 258. 258. 258. 258. 261. 261. 262. 347. 348. 348. 348. 348. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 358. 358. 360. 361. 361. 361. 361. 361. 361. 362. 362. 362. 362. 362. 367. 367. 367. 367. 369. 370. 370. 370. 370. 370. 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. 375. 375. 375. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 378. 378. 378. 378. 378. 378. 379. 380. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 387. 387. 387. 389. 389. 389. 389. 389. 389. 390. 390. 390. 390. 392. 392. 392. 392. 392. 392. 397. 397. 397. 397. 398. 398. 398. 398. 398. 399. 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. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 407. 407. 414. 417. 417. 418. 418. 418. 419. 422. 422. 422. 422. 422. 422. 422. 422. 424. 585. 585. 585. 585. 587. 587. 587. 587. 587. 587. 587. 587. 587. 587. 600. 600. 600. 600. 600. 600. 600. 600. 600. 600. 600. 602. 602. 602. 602. 602. 603. 603. 603. 603. 603. 603. 604. 604. 604. 604. 604. 604. 604. 605. 605. 605. 605. 605. 614. 615. 616. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 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. 619. 619. 619. 624. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 634. 634. 634. 634. 634. 640. 640. 641. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 657. 657. 657. 657. 657. 657. 657. 663. 663. 663. 663. 663. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 665. 665. 665. 665. 667. 667. 667. 667. 667. 667. 669. 670. 670. 670. 670. 670. 670. 670. 670. 670. 671. 671. 671. 671. 673. 673. 673. 823. 823. 823. 823. 823. 823. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 827. 828. 828. 828. 828. 828. 828. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 832. 832. 833. 841. 841. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 929. 929. 929. 940. 940. 940. 940. 940. 940. 940. 954. 954. 954. 954. 954. 955. 956. 956. 956. 956. 966. 966. 966. 966. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 969. 969. 969. 969. 969. 969. 969. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 973. 976. 977. 977. 977. 977. 978. 978. 978. 979. 979. 979. 979. 980. 980. 980. 980. 980. 980. 980. 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988.1002.1002.1002.1002.1002.1002.1002.1002.1002.1012.1012.1012.1012.1014.1014.1015.1015.1015.1015.1015.1015.1016.1016.1016.1017.1017.1017.1017.1018.1019.1019.1019.1019.1110.1110.1110.1110.1110.1110.1110.1110.1111.1115.1118.1119.1119.1119.1119.1119.1119.1124.1124.1124.1124.1124.1124.1124.1124.1124.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1129.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1135.1135.1139.1139.1140.1140.1140.1140.1140.1140.1141.1141.1141.1141.1141.1142.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1145.1145.1145.1146.1146.1146.1147.1147.1147.1147.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1154.1154.1155.1155.1155.1155.1155.1155.1155.1155.1158.1158.1158.1158.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1169.1169.1169.1169.1169.1169.1181.1181.1181.1181.1183.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1360.1360.1360.1360.1360.1360.1360.1360.1360.1362.1362.1362.1362.1363.1366.1371.1371.1371.1371.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1378.1381.1381.1381.1381.1381.1381.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1383.1383.1389.1390.1391.1391.1391.1391.1391.1391.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1414.1415.1415.1415.1419.1420.1420.1420.1420.1421.1421.1421.1421.1421.1421.1421.1422.1424.1424.1424.1424.1424.1424.1427.1427.1427.1427.1427.1427.1427.1427.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1429.1429.1429.1429.1429.1429.1429.1429.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: 45 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.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 1m26.764s user 0m23.791s sys 0m0.625s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m43.676s user 0m21.484s sys 0m0.558s Creating box around spheres Creating chemgrid maps real 0m41.979s user 0m12.376s sys 0m0.198s Atomic solvent excluded volume calculations underway FORTRAN STOP real 70m25.545s user 24m15.492s sys 0m0.151s 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.