Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-22.c.bkslab.org du2 starts 1 molecule processed, 0 errors first try already in then inzinc count is 0 bzcat: Can't open input file 89: No such file or directory. bzcat: Can't open input file 07: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. count is 0 nothing to compress bzcat: Can't open input file 89: No such file or directory. bzcat: Can't open input file 07: No such file or directory. 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 0m22.533s user 0m0.246s sys 0m0.118s 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 0:1306 spheres. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 68. 68. 68. 68. 69. 69. 69. 69. 69. 71. 71. 71. 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. 73. 73. 73. 75. 75. 75. 75. 75. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 191. 191. 191. 201. 201. 201. 201. 201. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 204. 204. 204. 204. 204. 204. 204. 207. 207. 207. 207. 207. 207. 207. 207. 207. 211. 212. 212. 212. 212. 212. 212. 212. 212. 213. 213. 213. 213. 213. 213. 213. 213. 214. 214. 214. 214. 214. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 218. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 221. 221. 221. 221. 221. 221. 222. 222. 222. 222. 222. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 237. 237. 237. 237. 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640. 640. 640. 641. 641. 641. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 643. 643. 643. 645. 645. 645. 645. 645. 645. 647. 647. 648. 648. 648. 648. 648. 648. 648. 648. 648. 651. 651. 798. 798. 798. 798. 800. 800. 800. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 802. 802. 802. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 803. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 804. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 805. 807. 807. 807. 816. 816. 816. 816. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 820. 820. 820. 820. 820. 820. 820. 820. 820. 820. 820. 820. 820. 916. 917. 917. 917. 917. 917. 917. 917. 917. 917. 917. 917. 917. 931. 931. 931. 931. 932. 933. 933. 933. 933. 933. 942. 943. 943. 943. 943. 943. 944. 944. 944. 944. 944. 944. 944. 944. 944. 944. 944. 944. 946. 946. 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984.1079.1079.1080.1080.1080.1080.1080.1081.1081.1082.1082.1082.1082.1082.1082.1082.1083.1084.1084.1086.1089.1089.1089.1089.1091.1091.1091.1091.1091.1091.1091.1091.1092.1092.1092.1092.1092.1092.1092.1093.1094.1095.1095.1095.1095.1095.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1096.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1099.1099.1099.1099.1099.1100.1100.1100.1100.1102.1102.1103.1105.1105.1105.1105.1105.1105.1105.1105.1105.1106.1106.1108.1108.1108.1111.1111.1112.1112.1112.1112.1112.1112.1112.1114.1114.1114.1114.1114.1114.1114.1119.1120.1120.1120.1120.1120.1124.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1129.1130.1134.1148.1148.1148.1148.1148.1148.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1302.1316.1318.1318.1318.1318.1318.1318.1319.1319.1319.1319.1319.1319.1319.1319.1325.1325.1327.1330.1330.1330.1332.1332.1332.1332.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1333.1334.1334.1334.1334.1334.1334.1334.1334.1334.1334.1334.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1348.1349.1349.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1357.1357.1357.1357.1358.1358.1373.1373.1373.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1383.1383.1383.1386.1386.1386.1386.1386.1386.1386.1386.1387.1387.1387.1387.1387.1387.1387.1387.1387.1389.1389.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: 38 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.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 2m4.820s user 0m28.601s sys 0m1.012s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m55.997s user 0m28.202s sys 0m1.031s Creating box around spheres Creating chemgrid maps real 0m38.596s user 0m11.099s sys 0m0.317s Atomic solvent excluded volume calculations underway FORTRAN STOP real 55m5.863s user 18m19.638s sys 0m0.252s 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.