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 0m2.329s user 0m0.423s sys 0m0.312s 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 0:1232 spheres. 66. 66. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 70. 70. 71. 71. 71. 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. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 76. 76. 76. 83. 83. 83. 84. 84. 84. 84. 84. 84. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 164. 164. 165. 165. 165. 165. 165. 166. 166. 166. 166. 166. 166. 166. 167. 167. 168. 168. 169. 169. 169. 169. 169. 182. 182. 182. 182. 182. 183. 183. 183. 183. 183. 183. 183. 197. 197. 197. 199. 199. 199. 199. 199. 199. 203. 209. 209. 209. 209. 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. 215. 215. 215. 219. 219. 220. 220. 220. 220. 221. 221. 222. 222. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 224. 228. 228. 228. 228. 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995.1008.1008.1008.1008.1008.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1111.1116.1117.1117.1117.1117.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1121.1121.1121.1121.1121.1122.1122.1122.1122.1122.1123.1123.1125.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1128.1128.1128.1128.1131.1131.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1141.1141.1142.1142.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1149.1149.1152.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1160.1160.1160.1160.1160.1162.1162.1162.1162.1162.1162.1162.1162.1167.1167.1167.1168.1168.1168.1168.1168.1168.1168.1169.1169.1172.1172.1172.1172.1172.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1174.1174.1174.1174.1174.1174.1174.1174.1175.1178.1182.1188.1188.1188.1188.1189.1192.1192.1195.1195.1195.1195.1214.1214.1214.1214.1217.1217.1217.1217.1217.1217.1217.1217.1217.1217.1218.1218.1218.1218.1218.1218.1218.1357.1357.1370.1370.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1373.1373.1374.1374.1374.1374.1374.1379.1379.1379.1379.1379.1379.1379.1379.1386.1386.1386.1386.1387.1388.1388.1389.1389.1389.1389.1391.1391.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1427.1427.1427.1427.1427.1427.1427.1427.1432.1432.1433.1433.1434.1434.1434.1434.1434.1434.1434.1434.1434.1434.1434.1434.1437.1437.1437.1437.1439.1439.1440.1440.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: 42 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.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 Creating DelPhi electrostatic grid real 0m58.704s user 0m36.928s sys 0m1.161s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m3.054s user 0m36.650s sys 0m1.398s Creating box around spheres Creating chemgrid maps real 1m4.770s user 1m3.803s sys 0m0.604s Atomic solvent excluded volume calculations underway FORTRAN STOP real 33m24.071s user 33m21.005s sys 0m0.290s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.