Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-26.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 0m34.104s user 0m0.233s 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 0:1561 spheres. 61. 61. 61. 62. 62. 62. 62. 68. 68. 68. 68. 68. 69. 69. 69. 69. 69. 69. 70. 70. 70. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 72. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 76. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 174. 174. 174. 184. 184. 188. 188. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 201. 201. 201. 201. 201. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 211. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 214. 214. 214. 214. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 218. 218. 222. 222. 222. 222. 222. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 224. 225. 225. 225. 225. 225. 225. 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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. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 613. 615. 615. 615. 615. 615. 616. 616. 616. 618. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 620. 620. 620. 620. 620. 620. 620. 625. 625. 625. 625. 626. 626. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 635. 635. 636. 636. 644. 644. 644. 644. 644. 644. 651. 657. 657. 657. 657. 658. 658. 659. 659. 659. 659. 659. 659. 659. 659. 659. 659. 659. 661. 661. 661. 664. 664. 664. 664. 664. 667. 667. 667. 667. 667. 804. 805. 805. 805. 805. 805. 805. 806. 806. 807. 807. 807. 807. 807. 807. 808. 808. 808. 808. 808. 808. 808. 808. 808. 812. 813. 813. 815. 815. 815. 815. 815. 815. 815. 816. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 818. 818. 818. 818. 818. 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992.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1006.1006.1006.1006.1006.1006.1008.1008.1008.1008.1008.1008.1008.1010.1010.1010.1101.1101.1101.1101.1101.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1106.1106.1106.1106.1106.1106.1110.1110.1110.1110.1110.1110.1110.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1123.1123.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1126.1126.1126.1132.1132.1132.1132.1132.1132.1132.1134.1134.1134.1134.1134.1134.1134.1134.1135.1135.1137.1137.1137.1137.1137.1137.1138.1138.1138.1138.1138.1138.1140.1140.1140.1140.1140.1146.1146.1146.1146.1146.1146.1146.1146.1146.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1152.1152.1152.1152.1152.1152.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1156.1156.1156.1158.1160.1160.1160.1160.1160.1160.1172.1172.1172.1325.1325.1325.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1340.1340.1340.1340.1340.1342.1342.1343.1343.1344.1344.1344.1345.1354.1356.1356.1356.1356.1356.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1359.1359.1359.1359.1359.1359.1359.1359.1361.1364.1364.1364.1364.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1374.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1390.1390.1390.1390.1390.1390.1390.1390.1397.1397.1397.1397.1397.1401.1401.1403.1403.1403.1403.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1405.1405.1405.1407.1407.1407.1407.1407.1407.1407.1407.1407.1407.1410.1410.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 1m50.580s user 0m27.014s sys 0m0.778s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m48.586s user 0m26.309s sys 0m0.789s Creating box around spheres Creating chemgrid maps real 0m38.003s user 0m9.845s sys 0m0.273s Atomic solvent excluded volume calculations underway FORTRAN STOP real 56m43.658s user 18m53.181s sys 0m0.181s 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.