Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-13.c.bkslab.org du2 starts 1 molecule processed, 0 errors convert.py (MDL SDF -> Isomeric SMILES): mols in: 0 mols out: 0 Total: 0 mols processed. mol2nam v1.9 Structure to Name Conversion OpenEye Scientific Software, February 2009 FATAL mmmdl_new: Could not seek to first structure for file ../6.sdf mmmdl_new failed. m2io_open failed for file C.mae. sed: can't read G.ism: No such file or directory E.mol2: No such file or directory. Warning: Unable to open "ref/F2.mol2" for reading molecules. Fatal: Cannot open: ref/F2.mol2 sed: can't read H.ism: No such file or directory /bin/mv: cannot stat `ref/F2.mol2': No such file or directory ref/F.mol2: No such file or directory. ref/D.sdf: No such file or directory. ref/D.sdf: No such file or directory. FATAL mmmdl_new: could not open file ../new.sdf: No such file or directory. mmmdl_new failed. m2io_open failed for file C.mae. sed: can't read G.ism: No such file or directory E.mol2: No such file or directory. FATAL mmmdl_new: could not open file ../new.sdf: No such file or directory. mmmdl_new failed. m2io_open failed for file C.mae. sed: can't read G.ism: No such file or directory E.mol2: No such file or directory. FATAL mmmdl_new: could not open file ../new.sdf: No such file or directory. mmmdl_new failed. m2io_open failed for file C.mae. sed: can't read G.ism: No such file or directory E.mol2: No such file or directory. F2.mol2: No such file or directory. F2.mol2: No such file or directory. F2.mol2: No such file or directory. F2.mol2: No such file or directory. first try already in then inzinc count is 0 bzcat: Can't open input file 41: No such file or directory. bzcat: Can't open input file 18: No such file or directory. bzcat: Can't open input file 42: No such file or directory. bzcat: Can't open input file 73: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 2 mols out: 2 Total: 2 mols processed. count is 0 bzcat: Can't open input file 43: No such file or directory. bzcat: Can't open input file 84: No such file or directory. bzcat: Can't open input file 44: No such file or directory. bzcat: Can't open input file 19: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 2 mols out: 2 Total: 2 mols processed. bzcat: Can't open input file 41: No such file or directory. bzcat: Can't open input file 18: No such file or directory. bzcat: Can't open input file 42: No such file or directory. bzcat: Can't open input file 73: No such file or directory. bzcat: Can't open input file 43: No such file or directory. bzcat: Can't open input file 84: No such file or directory. bzcat: Can't open input file 44: No such file or directory. bzcat: Can't open input file 19: 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 0m53.772s user 0m0.250s sys 0m0.092s 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 0:1419 spheres. 66. 66. 66. 66. 66. 66. 67. 67. 67. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 71. 71. 71. 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. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 75. 80. 80. 80. 84. 84. 84. 86. 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. 88. 88. 88. 88. 88. 88. 88. 88. 182. 182. 182. 183. 183. 183. 183. 183. 183. 183. 183. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 197. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 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. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 219. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 221. 221. 221. 221. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 224. 224. 228. 228. 228. 228. 229. 229. 229. 229. 229. 229. 230. 230. 230. 231. 231. 231. 231. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 245. 245. 245. 245. 245. 245. 245. 245. 245. 252. 252. 252. 252. 252. 252. 252. 252. 252. 252. 252. 252. 252. 252. 252. 252. 252. 255. 259. 259. 259. 259. 259. 259. 259. 259. 261. 346. 347. 347. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 354. 354. 354. 358. 358. 358. 359. 359. 360. 360. 362. 362. 362. 362. 362. 367. 367. 367. 367. 367. 367. 367. 368. 368. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 370. 370. 370. 370. 370. 370. 370. 370. 371. 373. 373. 373. 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. 374. 374. 374. 374. 374. 374. 374. 374. 374. 375. 375. 375. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 378. 378. 378. 378. 378. 379. 384. 384. 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. 387. 387. 387. 387. 387. 388. 388. 389. 389. 389. 389. 389. 390. 390. 390. 392. 392. 392. 392. 392. 397. 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. 404. 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. 407. 407. 407. 407. 407. 408. 410. 412. 412. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 587. 587. 587. 587. 587. 587. 587. 587. 587. 600. 600. 600. 600. 600. 600. 600. 600. 600. 600. 600. 600. 600. 600. 602. 602. 602. 602. 602. 602. 602. 603. 603. 603. 603. 603. 603. 604. 604. 604. 604. 605. 605. 605. 605. 605. 605. 614. 614. 616. 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. 617. 617. 617. 617. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 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. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 631. 631. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 640. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 649. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 657. 657. 657. 657. 657. 657. 661. 661. 663. 663. 663. 663. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 667. 667. 667. 667. 667. 667. 669. 670. 670. 670. 670. 824. 824. 824. 824. 824. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 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. 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. 833. 833. 833. 833. 833. 834. 842. 842. 842. 845. 845. 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. 846. 846. 846. 846. 846. 930. 930. 930. 940. 940. 941. 941. 941. 941. 941. 941. 941. 941. 948. 948. 948. 948. 948. 948. 955. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 967. 967. 967. 967. 967. 967. 968. 968. 968. 968. 968. 970. 970. 970. 970. 970. 970. 970. 970. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 977. 977. 977. 978. 978. 978. 978. 979. 979. 980. 980. 981. 981. 981. 981. 981. 981. 981. 981. 986. 986. 986. 986. 986. 988. 989. 989. 989. 989. 989.1003.1008.1008.1010.1010.1010.1010.1011.1013.1013.1013.1013.1013.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1016.1017.1017.1017.1018.1018.1018.1020.1020.1122.1122.1125.1125.1125.1125.1125.1125.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1134.1134.1134.1134.1134.1135.1135.1136.1136.1136.1136.1137.1137.1141.1141.1141.1141.1143.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1147.1147.1147.1147.1148.1148.1148.1148.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1156.1156.1156.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1165.1168.1170.1170.1170.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1362.1362.1362.1363.1364.1364.1364.1367.1369.1372.1373.1373.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1377.1379.1382.1382.1382.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1384.1384.1384.1384.1384.1384.1385.1390.1391.1392.1392.1398.1400.1400.1400.1400.1400.1400.1400.1400.1415.1415.1415.1415.1415.1420.1420.1421.1422.1422.1423.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: 34 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.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 1m28.091s user 0m21.991s sys 0m0.576s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m29.235s user 0m22.422s sys 0m0.592s Creating box around spheres Creating chemgrid maps real 0m52.775s user 0m14.498s sys 0m0.202s Atomic solvent excluded volume calculations underway FORTRAN STOP real 71m12.704s user 26m29.197s sys 0m0.155s 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.