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 first try already in then inzinc count is 0 bzcat: Can't open input file 73: No such file or directory. bzcat: Can't open input file 50: 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 73: No such file or directory. bzcat: Can't open input file 50: 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 0m2.029s user 0m0.377s sys 0m0.225s 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 0:1550 spheres. 122. 122. 122. 122. 122. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 127. 127. 127. 127. 127. 127. 127. 127. 127. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 218. 218. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 224. 224. 229. 229. 229. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 236. 236. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 240. 240. 240. 240. 240. 241. 241. 241. 241. 241. 241. 241. 241. 241. 241. 241. 241. 242. 242. 242. 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380. 380. 380. 387. 387. 387. 387. 387. 387. 387. 387. 387. 388. 388. 388. 388. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 396. 396. 396. 396. 396. 396. 396. 396. 396. 396. 530. 530. 530. 530. 530. 530. 530. 530. 530. 530. 530. 530. 530. 530. 530. 533. 533. 533. 533. 533. 533. 533. 533. 533. 533. 533. 533. 533. 533. 533. 533. 533. 533. 534. 534. 534. 534. 534. 535. 535. 535. 535. 535. 536. 536. 537. 539. 539. 542. 542. 542. 542. 543. 543. 543. 562. 562. 563. 563. 563. 563. 563. 563. 563. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 564. 570. 571. 571. 571. 571. 571. 571. 571. 571. 571. 572. 572. 572. 572. 574. 576. 576. 576. 576. 576. 576. 576. 576. 576. 578. 580. 580. 580. 580. 580. 595. 595. 595. 595. 595. 595. 595. 597. 597. 597. 597. 597. 598. 598. 598. 598. 598. 598. 598. 598. 598. 599. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 648. 649. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 651. 652. 652. 652. 652. 652. 652. 652. 652. 652. 652. 653. 653. 653. 653. 653. 653. 653. 653. 653. 654. 655. 655. 655. 655. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 659. 659. 662. 662. 662. 666. 666. 666. 666. 666. 666. 666. 666. 666. 666. 667. 667. 667. 668. 668. 668. 668. 668. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 676. 678. 678. 690. 786. 807. 807. 807. 807. 808. 808. 809. 809. 809. 809. 809. 809. 811. 811. 811. 811. 811. 824. 824. 824. 824. 825. 825. 825. 825. 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901.1211.1211.1211.1211.1211.1211.1211.1211.1211.1211.1211.1211.1211.1211.1211.1211.1212.1212.1212.1212.1212.1212.1212.1212.1212.1212.1216.1216.1217.1217.1217.1217.1217.1217.1217.1217.1217.1217.1217.1217.1217.1217.1217.1217.1217.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1224.1224.1225.1225.1225.1225.1225.1225.1225.1225.1225.1225.1225.1225.1225.1239.1239.1239.1239.1248.1248.1248.1248.1249.1249.1251.1251.1251.1251.1251.1251.1251.1251.1251.1251.1254.1254.1254.1254.1254.1254.1254.1280.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1282.1283.1283.1283.1284.1284.1284.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1300.1301.1301.1301.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1303.1303.1303.1303.1303.1303.1303.1303.1303.1303.1303.1303.1303.1303.1310.1310.1310.1310.1310.1310.1310.1310.1310.1310.1314.1314.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1319.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1323.1324.1324.1324.1324.1324.1324.1324.1324.1324.1324.1324.1325.1325.1325.1325.1325.1325.1325.1325.1326.1326.1326.1326.1326.1327.1327.1327.1327.1327.1329.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1332.1332.1332.1332.1332.1332.1334.1334.1334.1334.1334.1334.1334.1334.1336.1336.1336.1336.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1340.1340.1340.1340.1340.1341.1341.1341.1341.1341.1342.1342.1342.1342.1342.1342.1342.1342.1342.1343.1343.1343.1343.1343.1344.1344.1344.1344.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1346.1346.1346.1346.1346.1346.1346.1346.1346.1346.1346.1346.1346.1346.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1349.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.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 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 0m27.307s user 0m22.818s sys 0m0.565s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m24.857s user 0m21.439s sys 0m0.542s Creating box around spheres Creating chemgrid maps real 0m17.868s user 0m16.748s sys 0m0.278s Atomic solvent excluded volume calculations underway FORTRAN STOP real 30m10.434s user 30m9.686s sys 0m0.124s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar failed to get similars