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 0m2.033s user 0m0.364s sys 0m0.219s 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 0:1513 spheres. 66. 66. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 70. 71. 71. 71. 71. 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. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 75. 76. 83. 84. 84. 85. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 162. 164. 165. 165. 165. 165. 165. 166. 166. 167. 167. 167. 167. 167. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 170. 170. 172. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 197. 197. 197. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 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987.1001.1006.1006.1006.1011.1013.1014.1014.1014.1014.1014.1014.1014.1015.1015.1015.1015.1016.1016.1016.1017.1018.1104.1104.1104.1104.1104.1104.1104.1104.1108.1108.1109.1109.1109.1109.1109.1109.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1113.1113.1113.1113.1114.1114.1114.1114.1114.1114.1114.1115.1116.1116.1116.1116.1117.1117.1117.1118.1118.1118.1118.1118.1118.1118.1118.1118.1120.1120.1120.1120.1120.1123.1123.1123.1123.1123.1123.1123.1123.1123.1125.1125.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1133.1133.1133.1133.1133.1134.1134.1135.1135.1135.1135.1136.1136.1136.1136.1138.1138.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1140.1140.1140.1141.1145.1145.1146.1146.1146.1146.1146.1146.1146.1146.1148.1148.1148.1148.1148.1148.1148.1148.1148.1154.1154.1154.1154.1154.1157.1157.1157.1158.1158.1158.1158.1158.1158.1158.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1163.1168.1168.1168.1168.1168.1173.1174.1174.1174.1174.1174.1174.1174.1174.1175.1175.1175.1176.1176.1177.1177.1177.1177.1177.1177.1177.1177.1177.1177.1177.1177.1177.1178.1178.1178.1178.1178.1178.1178.1178.1178.1181.1181.1181.1181.1181.1181.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1200.1200.1200.1203.1203.1203.1204.1204.1204.1204.1204.1204.1205.1321.1321.1324.1325.1325.1325.1325.1325.1325.1325.1325.1325.1326.1327.1327.1327.1327.1327.1327.1327.1327.1351.1351.1351.1353.1355.1355.1355.1355.1355.1357.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1358.1358.1359.1359.1359.1359.1359.1359.1364.1364.1366.1369.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1374.1374.1376.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1381.1381.1381.1381.1386.1386.1389.1389.1396.1396.1396.1412.1418.1419.1419.1419.1419.1419.1419.1419.1419.1420.1422.1422.1422.1422.1424.1424.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1426.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: 54 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. 52. 53. 54.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 1m8.825s user 0m46.348s sys 0m2.113s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 1m3.455s user 0m49.262s sys 0m1.979s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 1m28.907s user 1m10.007s sys 0m1.284s Atomic solvent excluded volume calculations underway FORTRAN STOP real 26m47.779s user 26m47.191s sys 0m0.200s 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.