Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-07.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 98: No such file or directory. bzcat: Can't open input file 51: 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 50: No such file or directory. bzcat: Can't open input file 54: 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 98: No such file or directory. bzcat: Can't open input file 51: No such file or directory. bzcat: Can't open input file 50: No such file or directory. bzcat: Can't open input file 54: 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 0m6.587s user 0m0.274s sys 0m0.117s 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 0:1323 spheres. 66. 66. 66. 66. 67. 67. 68. 69. 69. 69. 69. 69. 69. 69. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 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. 84. 84. 84. 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. 172. 172. 172. 172. 182. 182. 182. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 199. 199. 199. 199. 199. 199. 199. 199. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 216. 216. 219. 221. 221. 221. 221. 221. 221. 221. 222. 223. 223. 223. 223. 223. 223. 223. 228. 228. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 245. 245. 245. 245. 245. 245. 245. 245. 245. 355. 355. 355. 355. 355. 355. 355. 355. 356. 356. 356. 356. 356. 360. 360. 360. 360. 361. 362. 363. 363. 363. 363. 363. 363. 364. 364. 364. 364. 364. 364. 369. 369. 369. 369. 369. 369. 369. 371. 371. 371. 371. 371. 371. 372. 372. 372. 372. 372. 372. 373. 374. 374. 374. 374. 374. 374. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 380. 380. 380. 381. 384. 384. 386. 386. 386. 386. 386. 386. 386. 387. 387. 387. 387. 387. 387. 388. 388. 391. 392. 392. 392. 392. 392. 394. 394. 394. 394. 394. 394. 394. 400. 400. 402. 403. 404. 404. 404. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 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673. 673. 673. 675. 675. 675. 675. 823. 826. 826. 826. 826. 826. 827. 827. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 831. 831. 831. 831. 831. 831. 831. 831. 831. 832. 832. 832. 832. 832. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 835. 835. 835. 844. 844. 844. 844. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 848. 848. 848. 848. 848. 932. 932. 932. 932. 932. 942. 942. 942. 951. 951. 951. 957. 957. 958. 959. 963. 969. 969. 969. 969. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 972. 972. 972. 972. 972. 972. 972. 972. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 976. 979. 981. 981. 981. 981. 981. 982. 982. 982. 982. 983. 983. 983. 983. 983. 983. 983. 983. 983. 983. 983. 985. 986. 986. 987. 987. 987. 988. 988. 988. 988. 988. 988. 988. 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992.1004.1004.1004.1004.1004.1004.1012.1012.1012.1012.1012.1015.1015.1015.1015.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1018.1021.1021.1021.1021.1115.1115.1115.1115.1115.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1120.1120.1123.1123.1123.1124.1124.1126.1127.1129.1129.1129.1129.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1133.1133.1134.1134.1134.1134.1134.1134.1134.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1141.1142.1142.1146.1146.1147.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1149.1149.1149.1151.1151.1151.1151.1151.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1154.1154.1154.1154.1154.1154.1154.1154.1154.1154.1154.1157.1160.1160.1160.1160.1160.1163.1163.1163.1164.1164.1164.1164.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1166.1166.1166.1167.1167.1169.1169.1170.1170.1170.1170.1174.1186.1186.1186.1186.1328.1328.1328.1330.1331.1331.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1334.1334.1334.1334.1334.1334.1334.1334.1334.1334.1334.1334.1334.1334.1334.1334.1334.1334.1341.1341.1341.1341.1341.1341.1341.1341.1341.1347.1347.1347.1349.1349.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1365.1365.1365.1365.1365.1365.1365.1366.1367.1371.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1381.1381.1383.1383.1383.1383.1387.1387.1387.1387.1387.1387.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1389.1389.1389.1395.1395.1395.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1404.1404.1404.1404.1404.1404.1404.1404.1404.1425.1425.1425.1425.1425.1426.1426.1426.1426.1426.1426.1429.1429.1429.1430.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1433.1433.1433.1435.1435.1435.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: 39 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.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 1m33.284s user 0m22.498s sys 0m0.548s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m41.323s user 0m22.478s sys 0m0.500s Creating box around spheres Creating chemgrid maps real 0m51.214s user 0m15.639s sys 0m0.196s Atomic solvent excluded volume calculations underway FORTRAN STOP real 84m16.695s user 28m47.039s sys 0m0.158s 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.