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 0m5.305s user 0m0.325s sys 0m0.238s 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 0:1363 spheres. 66. 66. 66. 66. 66. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 75. 75. 75. 84. 84. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 183. 183. 191. 191. 191. 191. 191. 197. 197. 197. 199. 199. 199. 199. 199. 199. 199. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 219. 220. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 228. 228. 228. 228. 228. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 347. 347. 347. 347. 347. 347. 351. 352. 352. 352. 353. 353. 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996.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1097.1097.1097.1097.1098.1098.1098.1098.1098.1098.1098.1098.1098.1098.1102.1105.1105.1106.1111.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1120.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1133.1133.1133.1133.1133.1134.1135.1135.1135.1135.1137.1137.1137.1139.1139.1139.1139.1140.1141.1141.1145.1145.1146.1146.1146.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1148.1148.1148.1148.1148.1148.1148.1148.1148.1150.1153.1153.1153.1154.1154.1154.1154.1154.1154.1154.1154.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1167.1343.1343.1343.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1346.1346.1346.1346.1346.1346.1346.1346.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1348.1348.1348.1348.1348.1348.1348.1348.1348.1348.1348.1348.1359.1359.1359.1359.1359.1359.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1362.1362.1362.1362.1362.1364.1367.1367.1367.1367.1367.1368.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1378.1378.1385.1385.1386.1386.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1407.1407.1407.1408.1408.1408.1408.1408.1408.1409.1411.1411.1411.1413.1413.1414.1414.1414.1414.1414.1414.1414.1414.1417.1417.1417.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... Detecting missing residue atoms... 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 1m29.060s user 0m56.002s sys 0m2.510s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m23.015s user 0m44.588s sys 0m2.184s Creating box around spheres Creating chemgrid maps real 1m6.003s user 1m5.035s sys 0m0.483s Atomic solvent excluded volume calculations underway FORTRAN STOP real 28m59.578s user 28m57.510s sys 0m0.142s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.