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 first try already in then inzinc count is 0 bzcat: Can't open input file 97: No such file or directory. bzcat: Can't open input file 40: 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 97: No such file or directory. bzcat: Can't open input file 40: 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 0m28.987s user 0m0.255s sys 0m0.102s 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 0:1243 spheres. 66. 66. 66. 66. 68. 68. 68. 69. 69. 69. 69. 69. 70. 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. 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. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 182. 182. 183. 183. 183. 183. 183. 183. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 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. 216. 219. 219. 220. 220. 220. 220. 220. 220. 220. 220. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 227. 227. 227. 228. 228. 228. 228. 228. 228. 228. 229. 229. 229. 229. 230. 231. 231. 231. 244. 244. 244. 244. 244. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 347. 347. 348. 348. 348. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 354. 358. 359. 359. 362. 362. 364. 367. 367. 367. 367. 367. 367. 367. 367. 368. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 370. 370. 370. 370. 370. 370. 371. 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. 376. 376. 376. 376. 376. 376. 376. 377. 378. 378. 378. 378. 378. 378. 378. 378. 379. 380. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 387. 388. 389. 390. 390. 390. 391. 392. 392. 392. 392. 392. 398. 398. 398. 398. 398. 398. 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. 407. 412. 412. 412. 412. 570. 570. 570. 570. 570. 571. 572. 572. 572. 572. 572. 572. 587. 602. 602. 602. 602. 602. 602. 603. 603. 603. 603. 604. 604. 605. 605. 609. 609. 609. 614. 616. 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. 617. 617. 617. 617. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 619. 624. 624. 624. 624. 624. 624. 624. 624. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 632. 633. 633. 634. 634. 634. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 657. 657. 657. 663. 663. 663. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 665. 667. 667. 667. 667. 667. 667. 669. 669. 669. 669. 670. 670. 670. 670. 670. 670. 670. 824. 824. 824. 824. 824. 824. 824. 824. 824. 827. 829. 829. 829. 829. 829. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 833. 833. 833. 833. 833. 833. 845. 845. 845. 846. 846. 941. 941. 941. 941. 957. 957. 957. 957. 957. 957. 957. 957. 957. 967. 967. 967. 967. 967. 967. 967. 967. 967. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 970. 970. 970. 970. 970. 970. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 977. 978. 978. 978. 978. 978. 978. 979. 979. 979. 979. 979. 979. 980. 980. 980. 980. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 984. 984. 984. 985. 985. 985. 986. 986. 986. 986. 986. 986. 988. 988. 988. 988. 988. 988.1001.1002.1002.1002.1002.1002.1013.1013.1013.1013.1013.1013.1013.1013.1015.1015.1015.1015.1017.1017.1017.1017.1018.1018.1018.1018.1018.1018.1019.1020.1020.1020.1105.1105.1111.1111.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1116.1116.1116.1116.1118.1120.1120.1122.1122.1125.1125.1125.1125.1125.1125.1125.1125.1126.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1128.1129.1129.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1135.1135.1135.1135.1135.1135.1136.1137.1137.1138.1138.1138.1140.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1142.1142.1142.1142.1143.1144.1146.1146.1146.1147.1147.1147.1147.1147.1147.1147.1147.1148.1148.1148.1148.1148.1149.1149.1149.1150.1150.1150.1150.1150.1150.1150.1150.1156.1156.1156.1156.1156.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1168.1168.1170.1170.1170.1170.1170.1170.1170.1182.1202.1202.1205.1205.1205.1205.1205.1207.1207.1207.1207.1327.1328.1328.1328.1329.1344.1345.1349.1355.1355.1358.1358.1358.1358.1358.1358.1360.1360.1360.1360.1360.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1361.1362.1362.1362.1372.1372.1373.1374.1374.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1382.1382.1383.1383.1383.1383.1383.1383.1383.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1390.1390.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1400.1400.1400.1400.1400.1400.1400.1400.1415.1415.1422.1422.1422.1422.1422.1422.1425.1425.1425.1425.1425.1427.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.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 1m10.399s user 0m22.360s sys 0m0.668s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m5.523s user 0m22.173s sys 0m0.640s Creating box around spheres Creating chemgrid maps real 0m32.890s user 0m13.940s sys 0m0.259s Atomic solvent excluded volume calculations underway FORTRAN STOP real 71m48.909s user 27m17.694s sys 0m0.087s 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.