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 0m1.994s user 0m0.333s sys 0m0.288s 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 0:1146 spheres. 62. 62. 62. 64. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 66. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 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. 71. 71. 71. 80. 80. 83. 83. 83. 83. 83. 83. 83. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 170. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 195. 195. 195. 196. 197. 197. 197. 197. 197. 197. 197. 197. 207. 207. 207. 207. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 210. 210. 210. 210. 210. 210. 210. 213. 213. 213. 213. 213. 218. 219. 219. 219. 219. 219. 219. 219. 221. 221. 221. 221. 221. 221. 221. 226. 227. 228. 228. 228. 228. 229. 229. 229. 229. 229. 236. 236. 236. 236. 236. 236. 236. 236. 243. 248. 248. 248. 248. 248. 248. 248. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 347. 348. 348. 348. 348. 348. 348. 348. 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993.1003.1006.1006.1006.1006.1009.1009.1010.1010.1010.1010.1010.1088.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1098.1098.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1104.1107.1107.1107.1107.1107.1107.1108.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1110.1110.1110.1110.1111.1113.1113.1113.1113.1113.1113.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1116.1116.1116.1116.1116.1116.1116.1116.1116.1118.1118.1118.1118.1119.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1127.1127.1128.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1132.1132.1132.1132.1132.1132.1132.1132.1138.1138.1138.1138.1138.1138.1138.1138.1138.1141.1141.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1144.1144.1144.1144.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1147.1147.1147.1147.1147.1147.1152.1152.1152.1152.1166.1166.1304.1304.1308.1308.1308.1308.1310.1310.1310.1310.1310.1310.1310.1310.1325.1338.1338.1338.1338.1338.1338.1340.1340.1340.1340.1341.1341.1341.1341.1342.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1362.1362.1362.1362.1363.1363.1363.1363.1363.1363.1363.1363.1363.1363.1363.1364.1364.1364.1364.1364.1364.1364.1364.1364.1364.1364.1364.1365.1365.1365.1365.1368.1372.1372.1372.1372.1372.1372.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1395.1400.1401.1401.1402.1402.1402.1402.1402.1402.1402.1402.1402.1402.1402.1403.1405.1405.1405.1405.1405.1407.1407.1407.1408.1408.1408.1408.1408.1411.1411.1411.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 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 0m42.050s user 0m30.931s sys 0m1.314s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m52.999s user 0m32.864s sys 0m1.331s Creating box around spheres Creating chemgrid maps real 1m4.377s user 1m0.904s sys 0m0.514s Atomic solvent excluded volume calculations underway FORTRAN STOP real 29m49.922s user 29m49.563s sys 0m0.312s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 End of MakeDOCK sphere and grid generation.