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 0m1.276s user 0m0.210s sys 0m0.171s 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 0:1306 spheres. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 66. 68. 68. 68. 68. 69. 69. 69. 69. 69. 71. 71. 71. 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. 73. 73. 73. 73. 75. 75. 75. 75. 75. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 191. 191. 191. 201. 201. 201. 201. 201. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 202. 204. 204. 204. 204. 204. 204. 204. 207. 207. 207. 207. 207. 207. 207. 207. 207. 211. 212. 212. 212. 212. 212. 212. 212. 212. 213. 213. 213. 213. 213. 213. 213. 213. 214. 214. 214. 214. 214. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 218. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 221. 221. 221. 221. 221. 221. 222. 222. 222. 222. 222. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 237. 237. 237. 237. 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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: 38 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.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 0m39.936s user 0m26.085s sys 0m0.909s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m12.405s user 0m25.426s sys 0m0.715s Creating box around spheres Creating chemgrid maps real 0m12.771s user 0m8.241s sys 0m0.229s Atomic solvent excluded volume calculations underway FORTRAN STOP real 17m54.428s user 17m53.656s sys 0m0.104s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 End of MakeDOCK sphere and grid generation.