Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-14.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 42: No such file or directory. bzcat: Can't open input file 17: 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 43: No such file or directory. bzcat: Can't open input file 68: 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 42: No such file or directory. bzcat: Can't open input file 17: No such file or directory. bzcat: Can't open input file 43: No such file or directory. bzcat: Can't open input file 68: 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 0m26.837s user 0m0.201s sys 0m0.104s 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 0:1347 spheres. 197. 199. 199. 199. 199. 199. 199. 199. 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. 212. 212. 212. 213. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 219. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 222. 222. 222. 222. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 226. 227. 227. 228. 228. 228. 228. 228. 228. 228. 229. 229. 229. 229. 229. 229. 229. 229. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 232. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 323. 323. 323. 327. 327. 327. 327. 327. 327. 328. 328. 328. 328. 328. 328. 328. 328. 328. 328. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 330. 330. 330. 330. 330. 330. 330. 331. 331. 331. 331. 335. 335. 335. 335. 335. 337. 337. 337. 337. 337. 337. 337. 340. 344. 344. 344. 344. 344. 344. 344. 344. 344. 344. 344. 344. 344. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 347. 347. 347. 347. 350. 351. 351. 351. 351. 351. 351. 352. 352. 352. 352. 353. 353. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 355. 355. 355. 355. 355. 355. 355. 355. 355. 355. 355. 360. 360. 360. 362. 362. 362. 362. 362. 362. 362. 362. 363. 363. 363. 363. 363. 363. 363. 364. 365. 365. 365. 365. 365. 365. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 370. 377. 377. 377. 377. 377. 377. 377. 377. 377. 377. 377. 377. 377. 378. 378. 378. 378. 378. 378. 378. 378. 379. 379. 379. 379. 379. 379. 379. 379. 379. 379. 379. 379. 379. 379. 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557. 557. 557. 557. 557. 562. 563. 563. 563. 564. 564. 564. 564. 564. 565. 565. 579. 584. 584. 584. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 586. 587. 608. 609. 609. 609. 609. 609. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 611. 611. 611. 611. 611. 611. 611. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 614. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 618. 618. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 625. 625. 625. 625. 625. 625. 626. 626. 626. 626. 627. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 650. 650. 650. 650. 656. 656. 656. 656. 656. 656. 656. 657. 657. 657. 657. 657. 657. 658. 658. 660. 660. 660. 660. 660. 660. 662. 662. 662. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 664. 666. 666. 666. 666. 666. 666. 666. 666. 816. 817. 818. 818. 819. 819. 819. 819. 820. 820. 820. 822. 822. 822. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 826. 826. 827. 827. 834. 834. 834. 834. 835. 835. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 838. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 932. 933. 933. 933. 933. 933. 933. 933. 933. 934. 934. 942. 942. 942. 942. 942. 942. 942. 942. 942. 950. 950. 950. 950. 954. 954. 954. 954. 954. 954. 954. 954. 954. 954. 954. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 961. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 964. 964. 964. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 975. 975. 975. 978. 978. 978. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 980. 980. 980. 981. 981. 993. 993. 993. 993. 993. 993. 993. 993. 993. 993. 993. 993. 995. 995. 995. 995.1115.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1117.1117.1117.1117.1117.1117.1117.1117.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1120.1120.1120.1120.1120.1120.1120.1122.1122.1123.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1132.1132.1132.1132.1132.1133.1133.1133.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1136.1136.1151.1151.1151.1151.1156.1156.1346.1346.1346.1347.1347.1347.1347.1347.1347.1348.1348.1348.1348.1349.1353.1353.1353.1356.1359.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1365.1365.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1378.1378.1378.1378.1378.1378.1378.1378.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1394.1394.1394.1394.1394.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: 38 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.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 1m40.916s user 0m24.971s sys 0m0.763s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m44.347s user 0m24.607s sys 0m0.731s Creating box around spheres Creating chemgrid maps real 0m35.207s user 0m9.918s sys 0m0.269s Atomic solvent excluded volume calculations underway FORTRAN STOP real 53m4.466s user 18m15.960s sys 0m0.525s 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.