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 0m1.350s user 0m0.213s sys 0m0.177s 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 0:1244 spheres. 65. 65. 67. 67. 67. 67. 67. 67. 67. 67. 67. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 71. 71. 71. 71. 71. 71. 74. 74. 74. 74. 82. 82. 82. 83. 83. 83. 83. 83. 83. 83. 83. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 87. 182. 182. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 197. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 202. 207. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 209. 209. 209. 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. 215. 215. 215. 218. 219. 219. 219. 219. 219. 220. 220. 221. 221. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 227. 227. 227. 227. 228. 229. 229. 229. 229. 229. 229. 230. 230. 230. 231. 234. 244. 244. 244. 249. 249. 249. 249. 249. 249. 252. 252. 252. 346. 346. 346. 346. 346. 347. 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996.1002.1002.1002.1002.1002.1002.1002.1002.1002.1002.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1011.1011.1109.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1116.1116.1116.1116.1116.1117.1118.1120.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1136.1141.1141.1142.1142.1142.1142.1142.1142.1142.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1145.1145.1145.1145.1147.1147.1147.1147.1147.1147.1148.1148.1148.1148.1148.1149.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1151.1156.1156.1156.1156.1156.1159.1159.1159.1159.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1163.1163.1165.1165.1170.1170.1204.1205.1205.1206.1206.1206.1206.1206.1206.1206.1207.1324.1328.1343.1360.1360.1360.1360.1360.1361.1361.1361.1362.1362.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1382.1382.1382.1382.1382.1382.1382.1382.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1386.1386.1386.1386.1386.1386.1386.1386.1387.1387.1387.1387.1387.1387.1387.1387.1388.1388.1388.1388.1388.1388.1388.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1402.1402.1403.1403.1403.1403.1403.1403.1418.1418.1418.1418.1424.1424.1424.1424.1424.1424.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1426.1426.1426.1426.1428.1428.1428.1428.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1431.1431.1431.1431.1431.1431.1431.1431.1431.1434.1434.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 0m44.492s user 0m29.677s sys 0m1.086s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m7.041s user 0m29.201s sys 0m0.862s Creating box around spheres Creating chemgrid maps real 0m13.420s user 0m8.904s sys 0m0.260s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m7.385s user 18m6.239s sys 0m0.040s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.