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 0m36.828s user 0m0.331s sys 0m0.123s 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 0:1505 spheres. 79. 82. 82. 82. 82. 82. 82. 82. 84. 84. 84. 84. 85. 85. 85. 85. 86. 86. 86. 87. 87. 87. 87. 89. 89. 89. 89. 89. 89. 90. 90. 90. 90. 90. 90. 90. 90. 90. 90. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 92. 92. 92. 94. 94. 95. 95. 95. 103. 103. 103. 103. 107. 107. 107. 107. 107. 107. 107. 107. 107. 224. 224. 224. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 240. 242. 242. 242. 242. 242. 242. 242. 242. 242. 242. 242. 242. 255. 255. 255. 255. 255. 255. 256. 256. 256. 256. 256. 256. 256. 256. 256. 259. 259. 259. 259. 259. 259. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 267. 268. 268. 268. 269. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 272. 272. 272. 272. 272. 272. 277. 277. 277. 278. 278. 278. 278. 278. 278. 278. 278. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 280. 280. 280. 280. 280. 280. 280. 280. 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483. 483. 483. 483. 483. 483. 483. 483. 486. 486. 486. 486. 486. 486. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 488. 488. 488. 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. 489. 489. 489. 493. 497. 497. 497. 497. 514. 515. 546. 546. 546. 549. 692. 692. 692. 692. 692. 694. 694. 694. 694. 694. 694. 694. 730. 730. 730. 730. 730. 730. 730. 730. 730. 731. 731. 731. 731. 731. 731. 731. 731. 732. 739. 746. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 749. 749. 749. 749. 749. 751. 754. 754. 754. 754. 754. 754. 754. 754. 754. 754. 754. 754. 756. 756. 756. 756. 756. 756. 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830.1002.1002.1003.1003.1003.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1007.1007.1007.1007.1007.1007.1007.1008.1009.1010.1013.1013.1013.1013.1013.1013.1013.1013.1013.1013.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1015.1015.1017.1017.1017.1026.1026.1026.1026.1026.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1147.1147.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1163.1164.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1178.1178.1178.1178.1179.1182.1182.1182.1182.1182.1182.1182.1185.1185.1185.1185.1185.1185.1185.1185.1185.1185.1185.1185.1190.1190.1191.1194.1194.1194.1194.1194.1194.1194.1194.1195.1195.1195.1195.1195.1195.1195.1195.1200.1200.1200.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1204.1211.1211.1211.1211.1212.1219.1219.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1235.1235.1235.1235.1235.1235.1237.1237.1237.1238.1238.1238.1239.1239.1239.1239.1239.1239.1239.1338.1338.1338.1338.1338.1338.1339.1339.1339.1339.1339.1339.1339.1339.1340.1340.1344.1344.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1352.1352.1352.1354.1354.1354.1354.1358.1358.1358.1358.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1368.1368.1370.1370.1370.1370.1370.1370.1371.1371.1371.1371.1371.1371.1371.1371.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1377.1377.1377.1377.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1381.1388.1388.1388.1388.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1391.1391.1394.1394.1395.1395.1395.1395.1395.1395.1395.1395.1396.1396.1396.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1405.1405.1405.1405.1405.1407.1408.1408.1408.1408.1408.1408.1409.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1411.1411.1411.1411.1411.1411.1411.1412.1413.1415.1420.1420.1420.1420.1420.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1438.1438.1438.1438.1438.1438.1438.1439.1464.1464.1464.1464.1464.1464.1464.1464.1464.1464.1464.1468.1468.1468.1468.1472.1472.1472.1472.1472.1613.1614.1614.1615.1615.1615.1615.1615.1615.1615.1615.1615.1615.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1619.1619.1619.1619.1619.1619.1619.1633.1635.1635.1653.1653.1653.1653.1654.1654.1654.1654.1655.1655.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1667.1667.1669.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1672.1672.1672.1672.1677.1677.1679.1679.1679.1679.1679.1679.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1684.1694.1694.1694.1695.1695.1701.1701.1701.1701.1701.1701.1701.1701.1701.1701.1701.1711.1711.1711.1711.1711.1711.1711.1711.1711.1711.1711.1720.1720.1720.1726.1726.1726.1727.1727.1732.1732.1732.1732.1732.1732.1732.1732.1733.1733.1736.1736.1736.1736.1736.1736.1736.1738.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1740.1740.1740.1740.1740.1740.1740.1744.1753.1753.1753.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: 62 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.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 1m25.294s user 0m20.751s sys 0m0.516s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m53.364s user 0m22.465s sys 0m0.542s Creating box around spheres Creating chemgrid maps real 0m51.199s user 0m13.933s sys 0m0.206s Atomic solvent excluded volume calculations underway FORTRAN STOP real 84m8.471s user 27m54.574s sys 0m0.232s 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.