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 0m2.313s user 0m0.453s sys 0m0.292s 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 0:1369 spheres. 55. 57. 58. 59. 59. 59. 59. 60. 60. 60. 60. 60. 60. 60. 60. 60. 60. 60. 60. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 66. 66. 66. 66. 66. 66. 66. 66. 67. 69. 69. 71. 71. 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. 73. 73. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 76. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 85. 85. 85. 85. 85. 85. 85. 85. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 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. 172. 172. 183. 183. 197. 197. 197. 199. 199. 199. 199. 199. 199. 199. 199. 203. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 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987.1000.1000.1000.1000.1000.1006.1006.1006.1006.1011.1011.1011.1011.1013.1014.1014.1014.1014.1014.1014.1014.1014.1015.1015.1015.1017.1018.1018.1018.1018.1108.1108.1108.1108.1109.1109.1109.1109.1109.1109.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1114.1114.1114.1115.1116.1117.1117.1117.1118.1118.1118.1118.1118.1118.1118.1118.1118.1120.1120.1123.1123.1123.1123.1123.1123.1126.1126.1126.1126.1126.1126.1127.1127.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1134.1135.1140.1140.1140.1140.1140.1140.1141.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1143.1143.1143.1143.1143.1143.1145.1145.1146.1146.1146.1148.1148.1148.1148.1148.1148.1148.1153.1153.1154.1154.1154.1154.1154.1154.1154.1154.1156.1156.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1163.1163.1163.1168.1168.1168.1168.1168.1168.1181.1181.1181.1182.1182.1321.1325.1325.1325.1325.1325.1325.1326.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1346.1346.1346.1346.1346.1346.1346.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1358.1359.1359.1359.1360.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1374.1374.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1387.1387.1387.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1397.1397.1397.1397.1397.1397.1397.1397.1412.1412.1418.1418.1419.1419.1419.1419.1419.1419.1419.1419.1419.1419.1419.1420.1422.1422.1422.1422.1424.1424.1424.1424.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1426.1426.1426.1426.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 0m41.841s user 0m35.186s sys 0m1.495s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 0m59.741s user 0m35.385s sys 0m1.424s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 1m2.648s user 1m0.925s sys 0m0.451s Atomic solvent excluded volume calculations underway FORTRAN STOP real 31m53.044s user 31m50.443s sys 0m0.178s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASH 125 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 End of MakeDOCK sphere and grid generation.