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 1m47.813s user 0m0.267s sys 0m0.085s 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 0:1265 spheres. 68. 68. 69. 70. 72. 72. 72. 72. 72. 72. 72. 74. 74. 74. 74. 74. 74. 75. 175. 179. 179. 179. 179. 179. 179. 179. 179. 179. 182. 182. 182. 182. 187. 187. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 190. 196. 196. 196. 196. 197. 198. 198. 198. 198. 198. 198. 198. 205. 205. 208. 208. 208. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 211. 211. 211. 211. 211. 211. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 215. 218. 218. 219. 219. 219. 219. 219. 219. 219. 219. 220. 220. 220. 220. 220. 220. 220. 220. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 227. 227. 227. 227. 227. 228. 230. 230. 230. 230. 230. 230. 244. 244. 244. 244. 244. 244. 244. 244. 244. 249. 249. 249. 249. 249. 249. 249. 249. 251. 252. 252. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 349. 349. 349. 349. 349. 349. 350. 352. 352. 352. 353. 353. 353. 353. 353. 353. 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628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 629. 629. 629. 629. 629. 629. 629. 633. 636. 636. 636. 636. 636. 636. 637. 637. 637. 637. 637. 637. 637. 637. 644. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 645. 660. 660. 666. 666. 666. 666. 666. 666. 666. 666. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 670. 670. 670. 670. 672. 672. 672. 672. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 676. 676. 676. 676. 676. 691. 692. 827. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 830. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 835. 835. 835. 942. 942. 942. 950. 950. 950. 950. 950. 950. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 974. 974. 974. 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991.1004.1004.1004.1004.1004.1004.1109.1109.1112.1112.1112.1112.1112.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1117.1117.1117.1117.1117.1120.1120.1120.1121.1121.1121.1126.1126.1126.1126.1126.1128.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1135.1135.1135.1135.1135.1135.1135.1136.1136.1137.1139.1141.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1143.1144.1145.1145.1145.1148.1148.1148.1148.1148.1148.1148.1149.1149.1149.1149.1149.1149.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1157.1157.1157.1158.1158.1160.1160.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1163.1163.1163.1164.1164.1170.1170.1170.1170.1170.1170.1172.1172.1172.1172.1203.1206.1206.1206.1206.1206.1207.1207.1208.1208.1208.1208.1345.1359.1359.1359.1362.1362.1362.1363.1363.1363.1363.1363.1363.1363.1363.1363.1363.1363.1368.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1378.1378.1378.1378.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1387.1387.1387.1387.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1389.1389.1389.1389.1390.1390.1393.1397.1397.1397.1397.1397.1397.1397.1397.1397.1397.1403.1403.1403.1404.1405.1405.1405.1405.1405.1405.1405.1405.1405.1405.1405.1405.1420.1420.1420.1420.1421.1426.1426.1427.1427.1427.1427.1427.1427.1427.1427.1427.1427.1427.1428.1430.1430.1430.1432.1432.1433.1433.1433.1433.1433.1436.1436.1436.1436.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 1m30.473s user 0m21.329s sys 0m0.495s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m50.611s user 0m21.335s sys 0m0.543s Creating box around spheres Creating chemgrid maps real 0m46.999s user 0m13.941s sys 0m0.167s Atomic solvent excluded volume calculations underway FORTRAN STOP real 80m26.481s user 27m21.079s sys 0m0.260s 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.