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 0m2.552s user 0m0.418s sys 0m0.293s 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 0:1254 spheres. 66. 66. 66. 66. 67. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 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. 72. 72. 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. 75. 75. 75. 76. 76. 76. 76. 76. 84. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 197. 199. 199. 199. 199. 199. 199. 209. 209. 210. 210. 210. 210. 210. 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. 219. 219. 220. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 223. 223. 223. 223. 228. 228. 228. 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997.1002.1002.1002.1002.1002.1002.1002.1002.1002.1007.1007.1007.1009.1009.1009.1009.1009.1010.1010.1010.1010.1010.1010.1010.1012.1012.1012.1014.1014.1014.1014.1014.1014.1014.1098.1098.1100.1105.1105.1105.1105.1105.1105.1105.1106.1106.1106.1106.1106.1106.1106.1110.1110.1110.1110.1110.1111.1111.1111.1112.1112.1112.1113.1113.1113.1113.1113.1114.1114.1114.1114.1114.1114.1114.1116.1116.1116.1119.1119.1119.1119.1119.1119.1119.1122.1122.1122.1122.1123.1123.1123.1124.1124.1124.1124.1124.1124.1125.1125.1125.1125.1125.1125.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1129.1129.1129.1129.1130.1131.1132.1132.1132.1135.1137.1137.1137.1137.1137.1138.1138.1138.1138.1141.1141.1142.1142.1142.1142.1142.1142.1142.1142.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1149.1149.1150.1150.1150.1150.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1159.1164.1164.1176.1176.1176.1178.1339.1339.1352.1352.1352.1352.1352.1352.1352.1352.1352.1352.1352.1353.1354.1354.1354.1354.1354.1354.1354.1355.1355.1355.1355.1355.1355.1355.1355.1355.1357.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1371.1371.1371.1371.1371.1376.1376.1376.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1385.1385.1386.1386.1386.1386.1394.1394.1394.1394.1394.1394.1394.1409.1409.1415.1415.1415.1416.1416.1416.1416.1416.1416.1416.1416.1416.1416.1416.1419.1419.1419.1419.1422.1422.1422.1422.1422.1423.1423.1423.1425.1425.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: 54 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. 43. 44. 45. 46. 47. 48. 49. 50. 51. 52. 53. 54.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 we had to cook * HD2* Creating DelPhi electrostatic grid real 1m11.621s user 0m41.095s sys 0m1.863s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 0m56.697s user 0m49.876s sys 0m2.302s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 2m23.377s user 1m10.037s sys 0m1.007s Atomic solvent excluded volume calculations underway FORTRAN STOP real 35m57.703s user 35m54.492s sys 0m0.206s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ARG 41 has a net charge of 0.0400 End of MakeDOCK sphere and grid generation.