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 0m1.396s user 0m0.256s sys 0m0.227s 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 0:1336 spheres. 62. 62. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 67. 67. 67. 67. 67. 67. 67. 67. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 71. 71. 80. 80. 80. 80. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 176. 176. 176. 176. 176. 176. 191. 191. 191. 191. 191. 191. 191. 191. 191. 191. 191. 191. 202. 203. 203. 203. 203. 203. 203. 203. 203. 203. 203. 205. 205. 205. 205. 205. 205. 205. 205. 205. 205. 205. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 209. 209. 212. 212. 213. 213. 213. 213. 214. 214. 214. 214. 214. 214. 215. 215. 215. 215. 215. 215. 215. 221. 221. 223. 223. 223. 223. 223. 223. 223. 224. 224. 224. 224. 224. 224. 238. 238. 238. 238. 238. 238. 238. 238. 238. 333. 333. 339. 339. 339. 339. 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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: 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 0m43.221s user 0m30.051s sys 0m1.409s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m11.664s user 0m30.401s sys 0m1.277s Creating box around spheres Creating chemgrid maps real 0m15.580s user 0m8.760s sys 0m0.228s Atomic solvent excluded volume calculations underway FORTRAN STOP real 19m3.115s user 19m2.376s sys 0m0.023s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of -0.0090 !!! WARNING: LYS 70 has a net charge of 0.0730 !!! WARNING: LYS 106 has a net charge of 0.1210 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 154 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.1210 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of -0.0090 !!! WARNING: LYS 70 has a net charge of 0.0730 !!! WARNING: LYS 106 has a net charge of 0.1210 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 154 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.1210 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of -0.0090 !!! WARNING: LYS 70 has a net charge of 0.0730 !!! WARNING: LYS 106 has a net charge of 0.1210 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 154 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.1210 End of MakeDOCK sphere and grid generation.