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 0m2.001s user 0m0.363s 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 0:1390 spheres. 62. 62. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 66. 66. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 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. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 71. 71. 80. 80. 80. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 195. 195. 195. 197. 197. 197. 197. 197. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 210. 210. 210. 210. 213. 213. 213. 213. 217. 217. 218. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 219. 220. 221. 221. 221. 221. 221. 221. 226. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 228. 228. 228. 228. 228. 228. 229. 229. 229. 229. 229. 229. 229. 229. 229. 229. 229. 233. 243. 248. 248. 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998.1084.1085.1086.1087.1087.1087.1087.1090.1090.1090.1090.1090.1090.1091.1091.1091.1091.1091.1091.1091.1091.1091.1091.1091.1091.1091.1091.1091.1095.1095.1099.1099.1099.1099.1099.1099.1099.1099.1104.1104.1104.1104.1104.1104.1106.1106.1106.1106.1107.1107.1107.1107.1107.1107.1107.1107.1107.1107.1108.1109.1109.1109.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1113.1113.1113.1113.1113.1113.1113.1113.1113.1115.1115.1115.1121.1123.1123.1123.1123.1123.1123.1123.1123.1123.1123.1123.1123.1123.1123.1123.1123.1124.1124.1124.1126.1126.1126.1126.1126.1126.1126.1126.1126.1127.1127.1127.1127.1129.1129.1129.1129.1129.1129.1135.1135.1135.1135.1135.1135.1135.1135.1138.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1141.1141.1141.1141.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1144.1144.1144.1144.1144.1149.1149.1149.1149.1149.1157.1157.1177.1177.1177.1180.1180.1180.1180.1180.1180.1180.1181.1182.1182.1182.1182.1332.1332.1332.1332.1334.1334.1335.1335.1335.1335.1336.1336.1336.1336.1336.1336.1336.1336.1336.1337.1337.1337.1347.1347.1347.1348.1348.1348.1348.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1353.1353.1353.1353.1353.1353.1353.1356.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1359.1359.1359.1362.1364.1364.1364.1364.1364.1364.1364.1366.1366.1366.1366.1366.1366.1366.1366.1366.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1389.1389.1389.1394.1395.1395.1395.1395.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1397.1397.1397.1397.1399.1399.1399.1399.1399.1402.1402.1402.1402.1402.1402.1403.1403.1403.1403.1403.1405.1405.1405.1405.1405.1405.1405.1405.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: 47 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.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... Detecting missing residue atoms... Filling missing side chains using Prime... 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 0m30.139s user 0m26.118s sys 0m0.647s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m27.984s user 0m26.194s sys 0m0.591s Creating box around spheres Creating chemgrid maps real 0m17.174s user 0m16.645s sys 0m0.220s Atomic solvent excluded volume calculations underway FORTRAN STOP real 34m52.651s user 34m51.795s sys 0m0.134s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.