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 0m2.011s user 0m0.346s sys 0m0.300s 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 0:1245 spheres. 62. 62. 62. 62. 63. 63. 64. 64. 64. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 66. 66. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 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. 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. 71. 71. 80. 80. 80. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 83. 84. 84. 84. 170. 171. 171. 171. 171. 171. 171. 171. 171. 171. 171. 171. 171. 171. 171. 171. 171. 171. 171. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 179. 179. 179. 179. 179. 179. 185. 185. 186. 186. 186. 186. 186. 186. 186. 186. 186. 191. 191. 191. 191. 191. 191. 191. 191. 191. 194. 194. 194. 194. 194. 194. 194. 194. 194. 194. 194. 194. 194. 194. 197. 197. 197. 197. 198. 198. 198. 198. 198. 198. 198. 198. 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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: 13 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13.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 0m37.535s user 0m32.186s sys 0m1.270s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m52.438s user 0m32.553s sys 0m1.290s Creating box around spheres Creating chemgrid maps real 1m7.311s user 1m5.370s sys 0m0.610s Atomic solvent excluded volume calculations underway FORTRAN STOP real 31m23.342s user 31m20.541s sys 0m0.322s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: GLN 7 has a net charge of 0.0170 !!! 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 55 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: VAL 82 has a net charge of -0.0120 !!! WARNING: GLN 106 has a net charge of 0.0170 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! 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 154 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 !!! WARNING: VAL 181 has a net charge of -0.0120 !!! WARNING: GLN 7 has a net charge of 0.0170 !!! 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 55 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: VAL 82 has a net charge of -0.0120 !!! WARNING: GLN 106 has a net charge of 0.0170 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! 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 154 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 !!! WARNING: VAL 181 has a net charge of -0.0120 !!! WARNING: GLN 7 has a net charge of 0.0170 !!! 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 55 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: VAL 82 has a net charge of -0.0120 !!! WARNING: GLN 106 has a net charge of 0.0170 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! 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 154 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 !!! WARNING: VAL 181 has a net charge of -0.0120 End of MakeDOCK sphere and grid generation.