Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-14.c.bkslab.org du2 starts 1 molecule processed, 0 errors first try already in then inzinc count is 0 nothing to compress count is 0 nothing to compress nothing to compress 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 0m30.291s user 0m0.251s sys 0m0.106s 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 0:1195 spheres. 68. 68. 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. 75. 75. 75. 181. 189. 189. 189. 189. 189. 189. 189. 189. 190. 190. 190. 190. 190. 190. 190. 190. 190. 196. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 208. 209. 209. 209. 209. 209. 209. 209. 209. 211. 211. 211. 211. 211. 211. 211. 211. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 215. 215. 218. 218. 219. 219. 219. 220. 220. 220. 221. 221. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 226. 227. 227. 227. 227. 227. 227. 227. 227. 227. 229. 229. 229. 229. 229. 230. 230. 230. 230. 230. 230. 243. 243. 243. 346. 346. 346. 346. 349. 352. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 354. 357. 357. 357. 357. 357. 357. 357. 357. 358. 358. 358. 358. 360. 360. 360. 360. 360. 360. 360. 360. 361. 361. 363. 366. 366. 366. 368. 368. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 370. 370. 370. 371. 371. 371. 371. 371. 371. 371. 371. 372. 372. 372. 372. 372. 372. 372. 372. 372. 372. 372. 372. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 376. 376. 376. 376. 376. 376. 376. 377. 377. 377. 379. 383. 383. 383. 383. 384. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 386. 386. 388. 388. 389. 389. 389. 389. 389. 389. 389. 389. 391. 391. 391. 391. 391. 391. 396. 397. 397. 397. 397. 398. 398. 399. 399. 401. 401. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 402. 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. 406. 406. 411. 411. 411. 411. 423. 423. 423. 423. 423. 423. 423. 425. 425. 425. 443. 446. 446. 446. 447. 447. 447. 447. 447. 447. 448. 448. 448. 448. 448. 448. 448. 585. 585. 585. 585. 601. 601. 601. 601. 602. 602. 602. 602. 602. 602. 602. 602. 602. 603. 614. 614. 615. 615. 615. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 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. 620. 620. 623. 623. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 626. 626. 626. 626. 626. 631. 631. 631. 631. 631. 633. 633. 633. 633. 639. 639. 639. 640. 640. 640. 640. 640. 655. 655. 655. 655. 656. 656. 661. 661. 661. 661. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 665. 665. 665. 665. 665. 667. 667. 668. 668. 668. 668. 668. 668. 668. 669. 669. 669. 671. 671. 671. 671. 681. 681. 681. 681. 681. 681. 681. 681. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 820. 820. 821. 821. 821. 823. 823. 823. 823. 823. 823. 823. 824. 825. 826. 826. 826. 826. 826. 826. 826. 826. 826. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 829. 829. 829. 829. 837. 838. 838. 838. 838. 839. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 934. 934. 934. 936. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 951. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 963. 963. 964. 964. 964. 964. 964. 964. 966. 966. 966. 966. 966. 966. 966. 966. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 970. 970. 970. 973. 973. 974. 974. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 981. 981. 982. 982. 982. 982. 982. 982. 982. 983. 984. 985. 985. 985. 986. 998. 998. 998.1100.1101.1101.1101.1101.1102.1102.1104.1107.1107.1108.1108.1108.1108.1108.1112.1112.1113.1115.1115.1115.1116.1123.1123.1123.1123.1123.1123.1123.1123.1123.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1137.1138.1138.1138.1138.1138.1138.1138.1138.1138.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1141.1141.1141.1141.1143.1143.1143.1143.1143.1143.1144.1144.1144.1144.1144.1144.1144.1144.1144.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1152.1152.1152.1152.1152.1153.1153.1157.1157.1157.1157.1158.1161.1161.1161.1166.1166.1166.1166.1178.1178.1178.1178.1201.1323.1323.1324.1324.1325.1325.1326.1326.1340.1354.1356.1356.1356.1356.1356.1356.1357.1357.1357.1357.1357.1357.1358.1363.1363.1370.1370.1370.1370.1370.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1375.1375.1375.1378.1378.1378.1378.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1384.1384.1384.1386.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1394.1394.1395.1410.1410.1410.1410.1410.1410.1412.1416.1416.1416.1416.1416.1417.1417.1417.1417.1417.1417.1417.1417.1417.1417.1418.1420.1420.1420.1423.1423.1423.1423.1423.1423.1423.1426.1426.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: 54 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. 42. 43. 44. 45. 46. 47. 48. 49. 50. 51. 52. 53. 54.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 1m29.714s user 0m20.852s sys 0m0.562s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m49.455s user 0m21.277s sys 0m0.534s Creating box around spheres Creating chemgrid maps real 0m51.206s user 0m14.141s sys 0m0.189s Atomic solvent excluded volume calculations underway FORTRAN STOP real 80m19.687s user 27m6.149s sys 0m0.219s 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.