Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-06.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 50: No such file or directory. bzcat: Can't open input file 45: 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 50: No such file or directory. bzcat: Can't open input file 45: 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 0m1.920s user 0m0.217s sys 0m0.126s 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. 68. 69. 69. 69. 69. 69. 69. 69. 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. 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. 182. 183. 183. 183. 183. 183. 183. 183. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 216. 219. 219. 220. 220. 220. 220. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 223. 223. 223. 228. 228. 228. 228. 228. 229. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 245. 245. 245. 245. 245. 245. 245. 255. 255. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 260. 260. 261. 262. 262. 262. 346. 346. 346. 346. 346. 351. 353. 353. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 358. 358. 358. 358. 358. 359. 360. 360. 360. 362. 362. 362. 362. 362. 364. 367. 367. 367. 367. 367. 367. 367. 369. 370. 370. 370. 370. 370. 370. 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. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 378. 378. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 387. 387. 387. 387. 389. 389. 389. 389. 389. 389. 389. 389. 389. 390. 390. 390. 392. 392. 392. 392. 392. 392. 392. 392. 392. 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. 403. 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. 405. 405. 405. 407. 407. 407. 408. 412. 412. 412. 412. 412. 412. 424. 424. 424. 424. 587. 587. 587. 587. 587. 587. 587. 587. 600. 600. 600. 600. 600. 600. 600. 602. 602. 602. 602. 602. 602. 602. 602. 603. 603. 603. 603. 603. 603. 603. 603. 603. 604. 605. 605. 605. 605. 614. 616. 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. 617. 617. 617. 617. 617. 617. 617. 617. 617. 618. 618. 618. 618. 618. 618. 618. 618. 618. 619. 624. 624. 624. 624. 624. 624. 624. 624. 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. 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. 626. 626. 633. 633. 633. 634. 634. 634. 634. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 657. 657. 657. 657. 657. 657. 657. 657. 663. 663. 663. 663. 663. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 667. 667. 667. 667. 667. 669. 669. 670. 670. 670. 670. 824. 824. 824. 824. 824. 826. 827. 827. 827. 827. 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. 830. 830. 830. 830. 830. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 834. 834. 842. 842. 842. 842. 842. 843. 843. 843. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 846. 846. 846. 846. 846. 846. 846. 930. 930. 930. 930. 940. 940. 940. 941. 941. 941. 941. 941. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 957. 967. 967. 967. 967. 967. 967. 967. 968. 968. 968. 970. 970. 970. 970. 970. 970. 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989.1003.1003.1003.1003.1003.1003.1008.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1013.1013.1013.1013.1013.1013.1016.1016.1016.1017.1018.1018.1020.1020.1020.1020.1020.1020.1104.1104.1104.1104.1104.1104.1104.1104.1104.1104.1104.1104.1104.1104.1104.1104.1109.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1112.1112.1112.1112.1116.1116.1116.1116.1116.1116.1116.1117.1117.1117.1117.1118.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1122.1122.1122.1125.1125.1125.1125.1127.1128.1128.1129.1129.1130.1131.1131.1131.1131.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1135.1136.1136.1136.1136.1137.1139.1139.1140.1140.1140.1140.1140.1140.1141.1141.1141.1141.1141.1141.1141.1142.1142.1142.1142.1142.1142.1142.1143.1143.1147.1147.1147.1147.1147.1148.1148.1148.1148.1148.1148.1148.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1151.1156.1156.1156.1156.1156.1156.1156.1156.1156.1158.1159.1159.1159.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1165.1165.1165.1165.1165.1165.1165.1170.1170.1170.1170.1170.1182.1182.1182.1184.1184.1328.1328.1328.1328.1328.1328.1328.1328.1328.1328.1328.1328.1328.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1358.1358.1358.1358.1358.1358.1358.1358.1360.1360.1360.1360.1360.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1362.1362.1362.1362.1362.1362.1362.1362.1363.1363.1363.1363.1364.1364.1372.1372.1372.1372.1372.1372.1372.1374.1374.1374.1374.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1377.1379.1382.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1390.1390.1390.1390.1390.1391.1391.1398.1398.1398.1398.1400.1400.1400.1400.1400.1415.1415.1415.1416.1416.1416.1416.1416.1416.1416.1421.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1425.1425.1425.1425.1425.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1431.1431.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 0m56.194s user 0m26.728s sys 0m0.794s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m55.915s user 0m27.449s sys 0m0.918s Creating box around spheres Creating chemgrid maps real 0m22.430s user 0m10.601s sys 0m0.340s Atomic solvent excluded volume calculations underway FORTRAN STOP real 38m35.074s user 19m26.488s sys 0m0.168s 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.