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 0m1.150s user 0m0.208s sys 0m0.125s 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... 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 0m44.233s user 0m27.831s sys 0m1.001s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m16.880s user 0m28.061s sys 0m0.980s Creating box around spheres Creating chemgrid maps real 0m12.395s user 0m8.582s sys 0m0.234s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m30.683s user 18m29.985s sys 0m0.072s 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 70 has a net charge of 0.0200 !!! WARNING: LYS 119 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 154 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 70 has a net charge of 0.0200 !!! WARNING: LYS 119 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 154 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 70 has a net charge of 0.0200 !!! WARNING: LYS 119 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 154 has a net charge of 0.0200 End of MakeDOCK sphere and grid generation.