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 0m1.213s user 0m0.179s sys 0m0.155s 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 0:1195 spheres. 68. 68. 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. 75. 75. 75. 181. 189. 189. 189. 189. 189. 189. 189. 189. 190. 190. 190. 190. 190. 190. 190. 190. 190. 196. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 208. 209. 209. 209. 209. 209. 209. 209. 209. 211. 211. 211. 211. 211. 211. 211. 211. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 215. 215. 218. 218. 219. 219. 219. 220. 220. 220. 221. 221. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 226. 227. 227. 227. 227. 227. 227. 227. 227. 227. 229. 229. 229. 229. 229. 230. 230. 230. 230. 230. 230. 243. 243. 243. 346. 346. 346. 346. 349. 352. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 354. 357. 357. 357. 357. 357. 357. 357. 357. 358. 358. 358. 358. 360. 360. 360. 360. 360. 360. 360. 360. 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998.1100.1101.1101.1101.1101.1102.1102.1104.1107.1107.1108.1108.1108.1108.1108.1112.1112.1113.1115.1115.1115.1116.1123.1123.1123.1123.1123.1123.1123.1123.1123.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1137.1138.1138.1138.1138.1138.1138.1138.1138.1138.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1141.1141.1141.1141.1143.1143.1143.1143.1143.1143.1144.1144.1144.1144.1144.1144.1144.1144.1144.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1152.1152.1152.1152.1152.1153.1153.1157.1157.1157.1157.1158.1161.1161.1161.1166.1166.1166.1166.1178.1178.1178.1178.1201.1323.1323.1324.1324.1325.1325.1326.1326.1340.1354.1356.1356.1356.1356.1356.1356.1357.1357.1357.1357.1357.1357.1358.1363.1363.1370.1370.1370.1370.1370.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1375.1375.1375.1378.1378.1378.1378.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1384.1384.1384.1386.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1394.1394.1395.1410.1410.1410.1410.1410.1410.1412.1416.1416.1416.1416.1416.1417.1417.1417.1417.1417.1417.1417.1417.1417.1417.1418.1420.1420.1420.1423.1423.1423.1423.1423.1423.1423.1426.1426.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 Adding all-atom hydrogens... Working on structure 1 Pre-treating metals... Done treating metals Adding hydrogens... Treating metals... Creating di-sulfur bonds... Finding het groups... Coloring atoms by element (green carbons in hets)... Running ProtAssign... using exhaustive mode will sample waters done with preparation Writing to file... DONE. Output file: rec.mae Removing non-polar hydrogens... Renaming polar hydrogens... 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 0m38.590s user 0m27.599s sys 0m1.197s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m3.324s user 0m28.024s sys 0m0.842s Creating box around spheres Creating chemgrid maps real 0m19.167s user 0m9.006s sys 0m0.287s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m47.340s user 18m45.914s sys 0m0.077s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.