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 0m1.156s user 0m0.202s sys 0m0.130s 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 0:1405 spheres. 54. 57. 57. 57. 58. 58. 58. 58. 58. 58. 58. 58. 58. 58. 58. 58. 59. 59. 59. 65. 65. 66. 66. 66. 66. 66. 66. 67. 67. 67. 67. 67. 67. 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. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 80. 81. 81. 82. 82. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 85. 85. 85. 85. 85. 85. 85. 85. 85. 85. 85. 158. 159. 160. 161. 161. 161. 161. 161. 161. 161. 161. 161. 161. 161. 161. 162. 162. 163. 163. 163. 163. 164. 164. 164. 164. 164. 164. 164. 164. 164. 164. 177. 177. 177. 177. 177. 177. 177. 177. 177. 177. 177. 184. 184. 184. 184. 184. 184. 184. 184. 184. 184. 184. 184. 184. 184. 184. 184. 193. 193. 193. 193. 193. 193. 193. 193. 193. 203. 204. 204. 204. 204. 204. 206. 206. 206. 206. 206. 209. 209. 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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: 36 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.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 0m46.873s user 0m30.653s sys 0m1.401s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m24.097s user 0m32.792s sys 0m1.534s Creating box around spheres Creating chemgrid maps real 0m12.685s user 0m8.882s sys 0m0.361s Atomic solvent excluded volume calculations underway FORTRAN STOP real 16m22.428s user 16m21.264s sys 0m0.070s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: LYS 7 has a net charge of 0.0730 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0730 !!! WARNING: LYS 142 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.0730 !!! WARNING: LYS 7 has a net charge of 0.0730 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0730 !!! WARNING: LYS 142 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.0730 !!! WARNING: LYS 7 has a net charge of 0.0730 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0730 !!! WARNING: LYS 142 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.0730 End of MakeDOCK sphere and grid generation.