Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-12.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 0m29.251s user 0m0.208s 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 0:1381 spheres. 68. 68. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 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. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 83. 83. 84. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 164. 164. 165. 165. 165. 165. 165. 166. 166. 166. 166. 167. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 170. 182. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 197. 197. 197. 199. 199. 199. 199. 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. 210. 210. 210. 210. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 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626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 627. 632. 632. 632. 632. 634. 634. 634. 634. 634. 634. 634. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 657. 657. 662. 663. 663. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 667. 667. 667. 667. 669. 669. 669. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 671. 671. 671. 673. 673. 824. 824. 824. 824. 824. 824. 824. 826. 827. 827. 827. 827. 827. 827. 827. 827. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 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. 833. 833. 833. 834. 834. 834. 842. 842. 842. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 846. 846. 846. 846. 846. 846. 846. 846. 846. 930. 930. 930. 930. 940. 941. 941. 941. 941. 941. 941. 941. 946. 946. 946. 946. 957. 957. 957. 957. 957. 957. 957. 957. 957. 961. 964. 964. 967. 967. 967. 967. 967. 967. 967. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 970. 970. 970. 970. 970. 970. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 974. 977. 978. 978. 978. 978. 979. 979. 979. 979. 979. 979. 979. 979. 979. 980. 980. 980. 980. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 986. 986. 986. 986. 988. 988. 988. 988. 989.1003.1003.1003.1003.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1013.1013.1013.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1016.1016.1016.1016.1016.1016.1016.1018.1018.1018.1019.1019.1020.1020.1111.1111.1111.1111.1111.1111.1111.1111.1112.1112.1116.1117.1117.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1122.1122.1122.1123.1125.1125.1125.1125.1125.1125.1125.1125.1128.1128.1128.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1135.1135.1135.1135.1135.1135.1135.1135.1135.1136.1136.1136.1137.1138.1138.1140.1140.1141.1141.1141.1141.1141.1141.1141.1141.1141.1142.1142.1143.1143.1148.1148.1148.1148.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1154.1154.1154.1154.1154.1154.1154.1154.1154.1154.1154.1155.1155.1155.1155.1155.1156.1156.1156.1156.1156.1156.1163.1163.1163.1163.1163.1175.1177.1177.1177.1177.1342.1342.1342.1342.1342.1342.1342.1342.1351.1351.1351.1351.1351.1351.1351.1351.1353.1353.1353.1353.1353.1353.1353.1353.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1355.1355.1356.1356.1356.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1370.1370.1370.1370.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1378.1383.1384.1384.1384.1384.1385.1385.1385.1385.1385.1385.1391.1391.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1408.1408.1414.1414.1414.1414.1415.1415.1415.1415.1415.1415.1415.1415.1415.1415.1416.1418.1418.1418.1418.1418.1421.1421.1421.1421.1421.1421.1421.1421.1422.1424.1424.1424.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: 56 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.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 1m47.617s user 0m25.686s sys 0m0.764s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m45.527s user 0m26.749s sys 0m0.740s Creating box around spheres Creating chemgrid maps real 0m41.563s user 0m10.240s sys 0m0.278s Atomic solvent excluded volume calculations underway FORTRAN STOP real 52m55.942s user 19m12.274s sys 0m0.174s 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.