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 0m1.188s user 0m0.215s sys 0m0.133s 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 0:1639 spheres. 63. 66. 66. 66. 66. 66. 66. 68. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 70. 70. 70. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 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. 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. 73. 73. 73. 75. 75. 75. 75. 75. 75. 76. 84. 84. 84. 84. 84. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 172. 182. 182. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 210. 210. 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. 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566. 566. 566. 566. 566. 566. 566. 566. 566. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 568. 575. 575. 575. 575. 575. 575. 575. 597. 597. 598. 598. 598. 598. 598. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 599. 600. 600. 600. 600. 600. 600. 600. 605. 607. 610. 612. 612. 612. 612. 612. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 620. 620. 620. 620. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 621. 622. 622. 622. 622. 622. 622. 622. 622. 622. 622. 622. 622. 630. 630. 630. 630. 630. 630. 630. 630. 630. 630. 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997.1005.1005.1005.1005.1106.1106.1106.1106.1107.1107.1107.1107.1107.1107.1107.1110.1110.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1113.1113.1113.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1117.1117.1117.1117.1120.1120.1120.1120.1120.1122.1122.1123.1123.1123.1123.1123.1123.1124.1124.1124.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1128.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1131.1131.1131.1131.1131.1133.1133.1133.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1137.1138.1139.1139.1140.1141.1141.1142.1142.1142.1142.1142.1143.1143.1143.1143.1144.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1150.1150.1150.1151.1151.1151.1151.1151.1151.1151.1151.1154.1154.1154.1154.1154.1154.1155.1155.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1161.1161.1161.1161.1164.1165.1165.1165.1165.1165.1165.1177.1179.1179.1179.1334.1334.1334.1334.1334.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1349.1351.1351.1351.1351.1351.1351.1351.1351.1351.1352.1352.1352.1352.1352.1352.1352.1358.1358.1358.1360.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1368.1368.1368.1368.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1374.1374.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1379.1381.1383.1383.1383.1388.1390.1390.1390.1390.1390.1390.1390.1398.1398.1398.1398.1405.1405.1405.1410.1410.1411.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1413.1415.1415.1415.1415.1415.1415.1418.1418.1418.1418.1418.1418.1418.1418.1419.1419.1419.1419.1419.1419.1419.1419.1419.1421.1421.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: 51 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. 48. 49. 50. 51.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 0m29.459s user 0m25.562s sys 0m0.926s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 0m59.016s user 0m24.101s sys 0m0.658s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 0m14.453s user 0m8.762s sys 0m0.217s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m51.081s user 18m49.528s 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.