Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-10.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 0m45.352s user 0m0.317s sys 0m0.133s 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 0:1457 spheres. 66. 66. 66. 69. 69. 69. 69. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 71. 73. 73. 74. 74. 74. 74. 74. 75. 75. 75. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 80. 80. 81. 82. 82. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 84. 85. 85. 85. 85. 85. 85. 85. 85. 85. 85. 85. 85. 85. 85. 85. 85. 85. 86. 86. 86. 86. 86. 86. 86. 86. 86. 87. 87. 87. 87. 87. 88. 88. 88. 89. 90. 90. 90. 90. 90. 90. 91. 91. 91. 91. 91. 91. 91. 92. 92. 92. 93. 93. 93. 93. 93. 93. 93. 93. 93. 93. 93. 93. 95. 95. 95. 95. 95. 95. 95. 95. 95. 95. 95. 95. 104. 104. 104. 104. 104. 104. 104. 104. 104. 105. 105. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 108. 108. 108. 108. 108. 108. 108. 109. 115. 115. 115. 115. 204. 204. 205. 205. 206. 206. 206. 206. 206. 206. 209. 210. 210. 210. 210. 210. 210. 210. 211. 211. 224. 225. 225. 225. 225. 225. 225. 225. 225. 241. 241. 241. 243. 243. 243. 243. 243. 243. 243. 243. 256. 256. 256. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 260. 260. 263. 263. 263. 263. 263. 263. 263. 263. 263. 263. 263. 268. 268. 268. 268. 268. 270. 270. 270. 271. 271. 271. 271. 271. 272. 272. 272. 272. 273. 273. 273. 273. 273. 273. 273. 278. 278. 278. 278. 279. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 281. 281. 281. 281. 281. 281. 281. 281. 281. 281. 290. 290. 290. 290. 298. 298. 298. 298. 298. 298. 423. 427. 427. 428. 428. 429. 430. 430. 430. 430. 431. 431. 432. 432. 432. 435. 436. 436. 436. 437. 437. 437. 437. 437. 440. 440. 440. 440. 446. 446. 446. 446. 446. 446. 448. 448. 453. 453. 453. 453. 453. 453. 453. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 455. 455. 455. 455. 455. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 459. 459. 459. 459. 459. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 468. 468. 468. 468. 469. 469. 469. 469. 471. 471. 471. 472. 472. 472. 473. 473. 473. 474. 474. 476. 476. 476. 476. 476. 476. 483. 483. 483. 483. 483. 487. 488. 488. 488. 488. 488. 488. 488. 488. 488. 488. 488. 488. 488. 488. 488. 488. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 490. 491. 498. 498. 498. 498. 498. 498. 712. 712. 712. 712. 730. 730. 730. 732. 732. 732. 732. 732. 733. 733. 733. 733. 734. 734. 734. 735. 739. 739. 739. 739. 739. 739. 739. 747. 748. 748. 748. 748. 748. 748. 748. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 750. 756. 756. 756. 756. 756. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 757. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 769. 769. 769. 769. 769. 769. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 778. 778. 778. 778. 778. 778. 778. 778. 778. 778. 778. 796. 796. 796. 796. 802. 803. 806. 808. 808. 808. 808. 808. 808. 810. 810. 810. 810. 810. 812. 812. 812. 812. 815. 815. 815. 815. 815. 815. 815. 815. 816. 816. 818. 821. 821. 821. 821.1003.1005.1005.1005.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1009.1009.1009.1009.1010.1010.1010.1010.1010.1011.1011.1011.1011.1013.1013.1013.1013.1013.1013.1013.1013.1013.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1015.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1016.1018.1018.1026.1027.1027.1027.1027.1027.1028.1028.1028.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1031.1031.1127.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1132.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1147.1147.1148.1148.1148.1148.1148.1148.1148.1148.1148.1164.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1179.1179.1179.1179.1179.1179.1179.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1183.1183.1183.1183.1186.1186.1186.1186.1186.1186.1186.1186.1186.1186.1186.1186.1186.1186.1186.1186.1191.1191.1192.1192.1192.1193.1193.1193.1194.1194.1194.1194.1194.1194.1195.1195.1195.1195.1195.1195.1196.1196.1196.1196.1196.1196.1201.1201.1201.1201.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1204.1204.1204.1221.1221.1221.1221.1221.1221.1221.1350.1350.1352.1353.1353.1353.1355.1355.1355.1355.1359.1359.1359.1359.1359.1360.1360.1361.1363.1363.1363.1363.1369.1369.1369.1369.1371.1372.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1378.1378.1378.1378.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1382.1382.1382.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1391.1391.1392.1394.1395.1396.1396.1396.1396.1396.1396.1396.1396.1398.1399.1399.1399.1399.1406.1406.1406.1406.1406.1406.1410.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1411.1412.1412.1412.1412.1412.1412.1412.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1413.1414.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1422.1654.1654.1654.1655.1655.1655.1655.1655.1655.1656.1656.1656.1657.1657.1657.1657.1657.1658.1660.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1673.1674.1674.1674.1674.1674.1674.1679.1679.1679.1679.1679.1679.1679.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1690.1690.1690.1690.1691.1691.1692.1692.1692.1692.1692.1692.1692.1692.1693.1701.1701.1701.1701.1701.1701.1701.1701.1701.1701.1701.1701.1701.1701.1701.1719.1719.1719.1719.1725.1729.1731.1731.1731.1731.1731.1731.1731.1731.1731.1733.1733.1733.1733.1733.1733.1735.1735.1735.1735.1735.1735.1735.1735.1735.1735.1738.1738.1738.1738.1738.1738.1738.1738.1739.1739.1739.1741.1741.1741.1741.1744.1744.1744.1744.1744.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: 57 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.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 1m35.354s user 0m20.610s sys 0m0.518s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m35.997s user 0m22.204s sys 0m0.596s Creating box around spheres Creating chemgrid maps real 0m47.578s user 0m13.756s sys 0m0.210s Atomic solvent excluded volume calculations underway FORTRAN STOP real 77m30.692s user 25m29.564s sys 0m0.078s 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.