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 0m2.192s user 0m0.402s sys 0m0.326s 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 0:1358 spheres. 66. 66. 69. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 185. 185. 185. 185. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 199. 201. 201. 201. 201. 201. 201. 201. 201. 201. 211. 211. 211. 211. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 214. 214. 214. 214. 214. 214. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 222. 223. 223. 223. 223. 225. 225. 225. 225. 225. 225. 225. 225. 225. 225. 225. 225. 225. 225. 225. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 231. 232. 232. 232. 232. 232. 232. 232. 232. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 240. 240. 240. 240. 240. 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993.1078.1078.1078.1079.1079.1079.1079.1079.1079.1079.1080.1085.1085.1085.1086.1086.1086.1086.1086.1086.1086.1086.1086.1086.1086.1090.1090.1090.1090.1090.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1096.1099.1099.1099.1099.1101.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1103.1104.1104.1104.1105.1105.1105.1105.1105.1105.1105.1105.1105.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1110.1111.1111.1112.1115.1115.1115.1115.1115.1116.1116.1116.1116.1117.1118.1118.1118.1118.1118.1118.1118.1118.1118.1119.1119.1119.1120.1121.1121.1121.1121.1121.1122.1122.1122.1122.1122.1122.1122.1122.1124.1124.1124.1124.1124.1129.1129.1129.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1132.1134.1134.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1136.1136.1136.1136.1136.1136.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1139.1139.1140.1140.1142.1142.1144.1144.1144.1144.1144.1144.1156.1309.1309.1309.1309.1324.1324.1324.1324.1326.1326.1326.1326.1326.1326.1327.1327.1327.1328.1328.1328.1328.1328.1328.1328.1328.1328.1328.1328.1329.1329.1329.1340.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1343.1343.1343.1343.1343.1345.1345.1348.1348.1348.1348.1348.1348.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1354.1358.1358.1358.1358.1358.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1381.1381.1381.1387.1387.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1389.1391.1391.1391.1391.1391.1391.1393.1394.1394.1394.1394.1394.1394.1395.1395.1395.1395.1395.1395.1397.1397.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: 43 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.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 0m44.751s user 0m33.755s sys 0m1.504s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m56.383s user 0m33.420s sys 0m1.226s Creating box around spheres Creating chemgrid maps real 1m1.976s user 1m0.030s sys 0m0.560s Atomic solvent excluded volume calculations underway FORTRAN STOP real 30m37.337s user 30m36.854s sys 0m0.204s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: LYS 140 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 138 has a net charge of 0.0200 !!! WARNING: LYS 140 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 138 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 End of MakeDOCK sphere and grid generation.