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 66: No such file or directory. bzcat: Can't open input file 66: 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 66: No such file or directory. bzcat: Can't open input file 66: 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 0m20.123s user 0m0.243s sys 0m0.107s 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 0:1361 spheres. 68. 69. 69. 69. 69. 69. 69. 69. 69. 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. 73. 73. 73. 73. 75. 75. 75. 76. 76. 84. 84. 87. 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. 183. 183. 197. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 209. 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. 216. 220. 220. 220. 220. 220. 220. 220. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 224. 226. 227. 227. 228. 228. 228. 228. 229. 231. 243. 244. 244. 244. 244. 244. 244. 244. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 347. 348. 348. 348. 348. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 358. 359. 361. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 364. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 368. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 370. 370. 370. 370. 370. 370. 371. 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. 374. 374. 374. 374. 374. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 378. 379. 380. 384. 384. 384. 384. 384. 384. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 387. 387. 387. 387. 389. 389. 389. 389. 389. 390. 390. 390. 391. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 393. 397. 397. 397. 398. 398. 398. 398. 399. 399. 399. 401. 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. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 407. 412. 412. 412. 412. 425. 566. 570. 570. 571. 571. 571. 572. 572. 572. 572. 591. 591. 591. 591. 591. 591. 591. 591. 600. 602. 602. 602. 603. 603. 603. 603. 603. 603. 603. 604. 604. 604. 605. 609. 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. 617. 617. 617. 617. 617. 617. 617. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 619. 621. 621. 624. 624. 624. 624. 624. 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. 632. 634. 634. 634. 634. 634. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 657. 657. 657. 657. 663. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 665. 665. 667. 667. 667. 667. 667. 667. 669. 669. 669. 669. 670. 670. 670. 670. 670. 673. 824. 824. 824. 824. 824. 824. 824. 827. 827. 827. 829. 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. 833. 833. 833. 833. 833. 834. 842. 842. 842. 842. 843. 843. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 930. 930. 930. 930. 941. 941. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 967. 967. 967. 967. 967. 967. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 970. 970. 970. 970. 970. 970. 970. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 978. 978. 979. 979. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 985. 986. 986. 986. 987. 988. 988. 988. 988. 988. 988. 988. 988. 989.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1008.1008.1008.1013.1013.1013.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1017.1018.1018.1019.1019.1019.1020.1105.1108.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1116.1116.1116.1116.1117.1117.1117.1117.1117.1119.1119.1120.1120.1120.1120.1122.1122.1122.1125.1125.1125.1125.1125.1125.1125.1125.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1129.1129.1129.1130.1130.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1135.1135.1135.1135.1136.1136.1136.1137.1137.1137.1138.1138.1138.1141.1141.1141.1141.1141.1141.1141.1141.1143.1143.1143.1143.1143.1143.1143.1143.1144.1144.1144.1144.1144.1147.1147.1148.1148.1148.1148.1148.1148.1148.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1155.1155.1156.1156.1156.1156.1156.1158.1158.1158.1159.1159.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1165.1165.1165.1170.1170.1170.1170.1170.1170.1170.1171.1171.1171.1184.1184.1184.1202.1202.1205.1205.1205.1205.1205.1205.1205.1206.1206.1206.1206.1207.1324.1328.1328.1328.1328.1328.1328.1328.1328.1328.1329.1330.1330.1330.1330.1330.1330.1330.1345.1349.1349.1349.1349.1349.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1360.1360.1360.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1361.1362.1363.1363.1363.1363.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1382.1382.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1384.1384.1384.1384.1384.1384.1384.1385.1385.1390.1390.1390.1391.1392.1392.1392.1392.1392.1392.1392.1392.1399.1399.1400.1400.1400.1400.1400.1400.1400.1415.1415.1421.1421.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1425.1425.1425.1425.1427.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1429.1431.1431.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 1m30.705s user 0m22.448s sys 0m0.588s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m8.153s user 0m23.219s sys 0m0.686s Creating box around spheres Creating chemgrid maps real 0m41.522s user 0m14.476s sys 0m0.270s Atomic solvent excluded volume calculations underway FORTRAN STOP real 76m30.420s user 27m26.443s 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.