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 0m1.172s user 0m0.215s sys 0m0.097s 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 0:1290 spheres. 66. 68. 68. 68. 68. 69. 69. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 72. 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. 73. 73. 73. 73. 73. 73. 75. 84. 84. 84. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 183. 183. 183. 183. 183. 183. 183. 183. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 219. 219. 220. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 227. 228. 228. 228. 228. 228. 229. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 245. 245. 245. 245. 245. 245. 245. 255. 255. 255. 255. 256. 256. 256. 256. 258. 258. 258. 258. 258. 258. 261. 261. 262. 347. 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988.1002.1002.1002.1002.1002.1002.1002.1002.1002.1012.1012.1012.1012.1014.1014.1015.1015.1015.1015.1015.1015.1016.1016.1016.1017.1017.1017.1017.1018.1019.1019.1019.1019.1110.1110.1110.1110.1110.1110.1110.1110.1111.1115.1118.1119.1119.1119.1119.1119.1119.1124.1124.1124.1124.1124.1124.1124.1124.1124.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1129.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1135.1135.1139.1139.1140.1140.1140.1140.1140.1140.1141.1141.1141.1141.1141.1142.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1145.1145.1145.1146.1146.1146.1147.1147.1147.1147.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1154.1154.1155.1155.1155.1155.1155.1155.1155.1155.1158.1158.1158.1158.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1169.1169.1169.1169.1169.1169.1181.1181.1181.1181.1183.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1360.1360.1360.1360.1360.1360.1360.1360.1360.1362.1362.1362.1362.1363.1366.1371.1371.1371.1371.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1378.1381.1381.1381.1381.1381.1381.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1383.1383.1389.1390.1391.1391.1391.1391.1391.1391.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1414.1415.1415.1415.1419.1420.1420.1420.1420.1421.1421.1421.1421.1421.1421.1421.1422.1424.1424.1424.1424.1424.1424.1427.1427.1427.1427.1427.1427.1427.1427.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1429.1429.1429.1429.1429.1429.1429.1429.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: 45 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.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 we had to cook * HD2* Creating DelPhi electrostatic grid real 1m7.966s user 0m33.270s sys 0m1.081s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 1m4.742s user 0m30.966s sys 0m0.793s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 0m11.842s user 0m8.777s sys 0m0.430s Atomic solvent excluded volume calculations underway FORTRAN STOP real 16m54.746s user 16m54.358s sys 0m0.097s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 25 has a net charge of -0.3190 End of MakeDOCK sphere and grid generation.