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 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 0m3.181s user 0m0.223s sys 0m0.122s 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 0:1593 spheres. 66. 66. 66. 66. 66. 66. 66. 66. 68. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 70. 71. 71. 71. 71. 71. 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. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 75. 75. 75. 75. 75. 75. 84. 84. 84. 84. 84. 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. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 172. 172. 180. 180. 180. 182. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 197. 197. 197. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 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. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 227. 227. 227. 227. 227. 227. 228. 228. 228. 228. 228. 228. 228. 228. 228. 229. 229. 229. 229. 229. 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. 243. 243. 243. 243. 243. 243. 243. 244. 244. 244. 245. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 259. 260. 261. 261. 261. 261. 261. 261. 262. 262. 262. 262. 262. 262. 262. 262. 262. 351. 355. 355. 355. 355. 355. 356. 356. 356. 356. 356. 356. 356. 356. 356. 360. 360. 362. 362. 363. 363. 363. 363. 363. 363. 363. 364. 366. 366. 367. 368. 369. 369. 369. 369. 369. 369. 369. 369. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 372. 372. 372. 372. 372. 372. 372. 372. 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. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 377. 377. 377. 377. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 379. 379. 379. 381. 381. 381. 384. 384. 384. 384. 385. 385. 385. 385. 385. 385. 385. 386. 386. 386. 386. 386. 386. 386. 386. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 389. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 391. 391. 391. 391. 391. 391. 391. 391. 391. 391. 392. 392. 392. 392. 392. 392. 392. 392. 393. 393. 394. 394. 394. 394. 394. 394. 394. 394. 394. 395. 395. 395. 395. 397. 397. 397. 398. 398. 398. 398. 398. 398. 399. 399. 399. 399. 400. 400. 411. 411. 431. 431. 431. 431. 431. 431. 434. 436. 436. 436. 436. 436. 436. 573. 573. 573. 578. 578. 578. 578. 578. 587. 587. 587. 587. 587. 587. 587. 587. 587. 587. 587. 588. 588. 589. 589. 590. 591. 592. 597. 597. 597. 601. 601. 601. 601. 602. 603. 603. 603. 603. 603. 603. 603. 604. 604. 604. 604. 604. 604. 604. 604. 604. 604. 604. 604. 604. 604. 604. 604. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 606. 606. 606. 608. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 617. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 625. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 642. 647. 648. 648. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 650. 652. 652. 652. 652. 652. 652. 654. 654. 655. 655. 655. 655. 655. 655. 655. 656. 656. 656. 658. 658. 658. 658. 809. 809. 809. 809. 809. 809. 809. 810. 811. 811. 811. 812. 812. 812. 812. 812. 812. 812. 813. 814. 814. 814. 814. 814. 814. 814. 814. 814. 814. 814. 814. 814. 814. 814. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 818. 818. 818. 818. 818. 818. 818. 818. 818. 827. 827. 827. 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. 830. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 915. 915. 915. 919. 923. 923. 925. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 940. 940. 940. 942. 942. 942. 942. 942. 942. 942. 942. 942. 952. 952. 952. 952. 952. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 953. 955. 955. 955. 955. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 962. 963. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 965. 965. 965. 965. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 969. 969. 970. 970. 970. 970. 970. 971. 971. 971. 971. 971. 971. 971. 971. 971. 972. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 974. 986. 986. 986. 986. 986. 986. 987. 987. 987. 987. 987. 987. 998.1001.1001.1001.1001.1001.1001.1002.1003.1004.1004.1004.1004.1004.1004.1004.1004.1005.1005.1005.1005.1005.1005.1095.1098.1098.1098.1098.1098.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1103.1105.1105.1105.1105.1106.1106.1106.1106.1106.1106.1106.1109.1109.1111.1111.1112.1112.1112.1112.1112.1112.1112.1112.1114.1114.1114.1114.1114.1114.1114.1114.1114.1115.1115.1115.1115.1115.1115.1115.1116.1116.1116.1116.1116.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1120.1120.1120.1120.1120.1120.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1122.1124.1124.1124.1124.1124.1127.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1129.1129.1129.1129.1129.1129.1129.1129.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1132.1132.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1136.1137.1137.1137.1137.1137.1137.1137.1137.1137.1138.1138.1140.1140.1140.1141.1141.1141.1141.1141.1141.1143.1143.1143.1154.1174.1174.1174.1174.1174.1177.1177.1178.1178.1179.1179.1179.1179.1179.1179.1179.1315.1315.1316.1321.1321.1321.1321.1321.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1331.1331.1331.1332.1332.1334.1335.1340.1340.1341.1341.1344.1346.1346.1346.1346.1346.1346.1346.1346.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1348.1348.1348.1348.1348.1348.1348.1348.1348.1348.1348.1348.1349.1351.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1355.1358.1360.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1369.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1385.1391.1391.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1393.1395.1395.1395.1395.1395.1397.1397.1397.1397.1397.1397.1397.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1399.1401.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: 66 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. 55. 56. 57. 58. 59. 60. 61. 62. 63. 64. 65. 66.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 1m2.057s user 0m24.650s sys 0m0.695s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m53.837s user 0m24.812s sys 0m0.710s Creating box around spheres Creating chemgrid maps real 0m19.678s user 0m10.085s sys 0m0.286s Atomic solvent excluded volume calculations underway FORTRAN STOP real 46m11.625s user 20m40.919s sys 0m0.276s 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.