Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-12.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 13: No such file or directory. bzcat: Can't open input file 25: 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 13: No such file or directory. bzcat: Can't open input file 25: 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 0m40.190s user 0m0.222s sys 0m0.114s 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 0:1223 spheres. 66. 66. 69. 69. 69. 69. 69. 69. 69. 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. 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. 75. 75. 76. 84. 84. 84. 87. 87. 87. 87. 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. 197. 197. 199. 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. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 219. 220. 220. 220. 221. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 226. 226. 226. 227. 227. 228. 228. 228. 228. 230. 231. 231. 244. 244. 244. 244. 244. 244. 341. 341. 342. 342. 347. 347. 347. 347. 347. 347. 348. 348. 348. 348. 352. 353. 353. 356. 356. 356. 356. 358. 361. 361. 361. 361. 361. 361. 361. 361. 363. 363. 363. 363. 364. 364. 364. 364. 364. 364. 364. 365. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 370. 372. 374. 378. 378. 378. 378. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 381. 381. 383. 383. 383. 383. 384. 384. 384. 385. 385. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 392. 392. 392. 392. 392. 392. 394. 395. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 398. 398. 398. 398. 398. 398. 398. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 401. 406. 406. 406. 560. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 566. 566. 566. 566. 566. 566. 585. 585. 585. 585. 596. 596. 596. 596. 596. 596. 597. 597. 597. 597. 597. 597. 598. 598. 603. 603. 603. 603. 603. 603. 603. 610. 610. 610. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 612. 612. 612. 612. 612. 612. 612. 612. 612. 613. 615. 618. 618. 618. 618. 618. 618. 618. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 628. 628. 628. 628. 628. 634. 634. 636. 636. 636. 651. 651. 651. 651. 651. 651. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 659. 659. 661. 661. 661. 661. 661. 661. 661. 663. 663. 663. 663. 663. 663. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 665. 665. 667. 667. 818. 818. 818. 818. 820. 823. 823. 823. 823. 823. 823. 824. 824. 824. 824. 824. 824. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 827. 827. 827. 827. 836. 836. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 840. 840. 840. 840. 840. 840. 840. 924. 924. 924. 935. 949. 951. 951. 951. 951. 951. 951. 951. 951. 951. 951. 961. 961. 961. 961. 961. 961. 961. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 967. 967. 967. 967. 967. 967. 971. 971. 972. 972. 972. 972. 973. 973. 973. 973. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 980. 980. 980. 980. 981. 982. 982. 982. 982. 982. 982. 982. 982. 982. 982. 982. 982. 983. 997. 997. 997. 997. 997.1007.1010.1010.1010.1010.1010.1011.1012.1012.1012.1013.1013.1014.1014.1099.1099.1100.1101.1104.1104.1105.1105.1105.1105.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1110.1110.1110.1110.1110.1110.1110.1110.1111.1111.1111.1111.1112.1113.1113.1113.1114.1114.1114.1114.1114.1114.1114.1116.1116.1116.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1121.1121.1122.1122.1122.1123.1123.1123.1124.1124.1125.1125.1125.1125.1125.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1130.1130.1130.1131.1134.1135.1135.1135.1135.1135.1135.1135.1136.1136.1137.1137.1138.1138.1138.1138.1138.1138.1138.1138.1138.1141.1141.1142.1142.1142.1142.1142.1142.1144.1144.1144.1144.1144.1144.1144.1144.1144.1149.1149.1149.1149.1150.1150.1152.1152.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1159.1159.1159.1159.1164.1164.1164.1164.1164.1172.1192.1195.1195.1195.1196.1196.1196.1197.1197.1314.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1320.1320.1320.1320.1320.1320.1339.1339.1345.1345.1345.1345.1345.1345.1345.1345.1348.1348.1348.1348.1348.1348.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1351.1351.1351.1351.1351.1351.1351.1352.1352.1352.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1367.1367.1367.1367.1367.1367.1372.1372.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1375.1375.1375.1382.1382.1382.1382.1382.1389.1390.1390.1390.1405.1405.1411.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1415.1415.1415.1415.1415.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1419.1421.1421.1421.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: 50 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.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 1m50.925s user 0m25.745s sys 0m0.793s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m48.919s user 0m27.486s sys 0m0.765s Creating box around spheres Creating chemgrid maps real 0m36.273s user 0m10.481s sys 0m0.298s Atomic solvent excluded volume calculations underway FORTRAN STOP real 55m15.058s user 18m11.235s 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.