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 0m29.562s user 0m0.222s sys 0m0.126s 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 0:1254 spheres. 66. 66. 66. 66. 67. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 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. 72. 72. 72. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 75. 76. 76. 76. 76. 76. 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. 88. 88. 88. 88. 88. 88. 88. 88. 88. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 197. 199. 199. 199. 199. 199. 199. 209. 209. 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. 219. 219. 220. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 223. 223. 223. 223. 228. 228. 228. 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658. 658. 658. 658. 658. 658. 658. 658. 658. 659. 661. 661. 661. 661. 663. 663. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 665. 665. 665. 665. 665. 665. 665. 667. 818. 818. 818. 821. 821. 821. 823. 823. 823. 823. 823. 823. 823. 823. 824. 824. 824. 824. 824. 824. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 827. 827. 827. 836. 836. 836. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 840. 840. 840. 840. 840. 840. 840. 840. 840. 924. 924. 924. 935. 949. 949. 949. 949. 951. 951. 951. 951. 961. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 964. 964. 964. 964. 964. 964. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 968. 972. 972. 972. 972. 972. 972. 973. 973. 973. 973. 973. 973. 975. 975. 975. 975. 975. 975. 975. 975. 980. 980. 980. 981. 981. 981. 982. 982. 982. 982. 982. 982. 983. 983. 983. 983. 997. 997. 997. 997.1002.1002.1002.1002.1002.1002.1002.1002.1002.1007.1007.1007.1009.1009.1009.1009.1009.1010.1010.1010.1010.1010.1010.1010.1012.1012.1012.1014.1014.1014.1014.1014.1014.1014.1098.1098.1100.1105.1105.1105.1105.1105.1105.1105.1106.1106.1106.1106.1106.1106.1106.1110.1110.1110.1110.1110.1111.1111.1111.1112.1112.1112.1113.1113.1113.1113.1113.1114.1114.1114.1114.1114.1114.1114.1116.1116.1116.1119.1119.1119.1119.1119.1119.1119.1122.1122.1122.1122.1123.1123.1123.1124.1124.1124.1124.1124.1124.1125.1125.1125.1125.1125.1125.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1129.1129.1129.1129.1130.1131.1132.1132.1132.1135.1137.1137.1137.1137.1137.1138.1138.1138.1138.1141.1141.1142.1142.1142.1142.1142.1142.1142.1142.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1149.1149.1150.1150.1150.1150.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1159.1164.1164.1176.1176.1176.1178.1339.1339.1352.1352.1352.1352.1352.1352.1352.1352.1352.1352.1352.1353.1354.1354.1354.1354.1354.1354.1354.1355.1355.1355.1355.1355.1355.1355.1355.1355.1357.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1371.1371.1371.1371.1371.1376.1376.1376.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1385.1385.1386.1386.1386.1386.1394.1394.1394.1394.1394.1394.1394.1409.1409.1415.1415.1415.1416.1416.1416.1416.1416.1416.1416.1416.1416.1416.1416.1419.1419.1419.1419.1422.1422.1422.1422.1422.1423.1423.1423.1425.1425.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 1m56.555s user 0m27.453s sys 0m0.785s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m48.515s user 0m28.238s sys 0m0.879s Creating box around spheres Creating chemgrid maps real 0m38.448s user 0m10.586s sys 0m0.254s Atomic solvent excluded volume calculations underway FORTRAN STOP real 51m7.434s user 19m0.119s sys 0m0.048s 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.