Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-23.c.bkslab.org du2 starts 1 molecule processed, 0 errors convert.py (MDL SDF -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. mol2nam v1.9 Structure to Name Conversion OpenEye Scientific Software, February 2009 convert.py (Tripos MOL2 -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. mid: No such file or directory. hi: No such file or directory. lo: No such file or directory. mid: No such file or directory. first try already in then inzinc count is 0 bzcat: Can't open input file 36: No such file or directory. bzcat: Can't open input file 74: 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 36: No such file or directory. bzcat: Can't open input file 74: 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 0m16.150s user 0m0.226s sys 0m0.108s 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 0:1412 spheres. 66. 66. 66. 67. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 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. 73. 75. 75. 75. 84. 87. 87. 87. 87. 87. 87. 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. 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. 197. 199. 199. 199. 199. 199. 199. 208. 209. 209. 209. 209. 209. 209. 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. 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. 215. 219. 220. 221. 221. 221. 221. 221. 222. 222. 222. 222. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 225. 228. 228. 228. 228. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 231. 232. 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. 253. 253. 253. 253. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 354. 354. 354. 358. 358. 358. 358. 358. 358. 359. 359. 359. 359. 359. 359. 360. 361. 361. 362. 362. 362. 362. 362. 362. 362. 365. 368. 368. 368. 368. 368. 368. 368. 369. 370. 371. 371. 372. 372. 372. 372. 372. 372. 372. 372. 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. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 377. 378. 378. 378. 378. 378. 378. 378. 383. 383. 383. 384. 384. 384. 386. 386. 386. 386. 386. 386. 386. 387. 388. 389. 389. 390. 390. 390. 391. 391. 391. 392. 398. 398. 401. 401. 401. 401. 402. 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. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 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. 405. 405. 407. 407. 408. 412. 424. 424. 424. 424. 424. 424. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 600. 602. 602. 602. 602. 603. 603. 603. 603. 603. 605. 605. 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. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 619. 619. 619. 624. 624. 624. 624. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 626. 626. 626. 626. 626. 626. 626. 626. 626. 632. 634. 634. 634. 634. 634. 634. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 650. 650. 650. 650. 650. 650. 657. 657. 663. 663. 663. 663. 664. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 667. 667. 667. 667. 667. 667. 668. 669. 669. 669. 669. 670. 670. 670. 670. 670. 670. 671. 671. 671. 671. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 824. 824. 824. 824. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 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. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 833. 833. 842. 845. 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. 940. 941. 941. 941. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 946. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 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. 968. 970. 970. 970. 970. 970. 970. 970. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 974. 974. 977. 978. 978. 979. 979. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 983. 983. 986. 986. 986. 987. 987. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 989. 989. 989. 989. 989. 989. 989. 989. 989. 990. 996. 996. 996. 996. 996. 996. 996.1003.1003.1003.1003.1003.1010.1010.1010.1010.1010.1011.1011.1011.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1115.1115.1116.1116.1116.1116.1116.1116.1116.1116.1116.1117.1117.1117.1117.1117.1120.1120.1120.1120.1120.1120.1122.1126.1126.1127.1129.1130.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1135.1135.1135.1136.1136.1137.1141.1141.1142.1142.1142.1144.1144.1144.1144.1144.1145.1145.1146.1146.1146.1146.1146.1146.1148.1149.1149.1156.1156.1156.1156.1156.1158.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1165.1165.1165.1165.1166.1170.1182.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1360.1360.1360.1361.1361.1361.1361.1361.1361.1363.1363.1363.1363.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1377.1377.1382.1382.1382.1382.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1392.1392.1392.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1408.1408.1415.1415.1415.1415.1416.1416.1416.1416.1421.1421.1421.1421.1421.1421.1421.1421.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1425.1425.1425.1425.1427.1428.1428.1428.1428.1428.1429.1429.1429.1429.1429.1429.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.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: 41 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.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 1m31.752s user 0m25.829s sys 0m0.766s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m43.073s user 0m25.003s sys 0m0.691s Creating box around spheres Creating chemgrid maps real 0m35.501s user 0m10.230s sys 0m0.260s Atomic solvent excluded volume calculations underway FORTRAN STOP real 41m8.729s user 19m13.737s sys 0m0.336s 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.