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 0m1.967s user 0m0.347s sys 0m0.218s 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 0:1641 spheres. 66. 66. 66. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 70. 70. 70. 70. 71. 71. 71. 71. 71. 71. 71. 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. 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. 83. 83. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 162. 162. 162. 162. 162. 163. 163. 164. 165. 165. 165. 165. 166. 166. 166. 166. 166. 166. 166. 166. 166. 167. 167. 167. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 169. 170. 170. 170. 172. 182. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 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938. 938. 938. 938. 938. 954. 954. 954. 954. 954. 954. 954. 954. 954. 964. 964. 964. 964. 964. 964. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 967. 967. 967. 967. 967. 967. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 974. 975. 975. 976. 976. 976. 976. 976. 976. 976. 976. 976. 976. 976. 977. 977. 977. 977. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 983. 983. 983. 984. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 986. 986. 986.1000.1000.1000.1010.1010.1013.1013.1013.1013.1013.1013.1013.1013.1013.1014.1014.1014.1016.1016.1016.1016.1017.1017.1101.1101.1103.1103.1103.1107.1107.1108.1108.1108.1108.1108.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1112.1112.1113.1113.1113.1113.1113.1116.1116.1117.1119.1119.1119.1119.1119.1122.1122.1122.1122.1122.1124.1124.1124.1126.1126.1126.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1132.1132.1133.1134.1134.1135.1137.1138.1138.1138.1138.1138.1138.1138.1138.1139.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1144.1144.1144.1145.1145.1145.1145.1145.1145.1145.1145.1147.1147.1147.1147.1147.1147.1147.1147.1153.1153.1153.1153.1153.1153.1153.1157.1157.1157.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1162.1167.1167.1167.1167.1167.1173.1173.1173.1173.1173.1173.1173.1174.1174.1175.1175.1175.1176.1176.1177.1180.1180.1180.1180.1180.1181.1181.1181.1181.1181.1181.1181.1181.1181.1181.1181.1181.1181.1181.1181.1199.1202.1202.1202.1202.1202.1203.1203.1203.1203.1204.1320.1320.1323.1324.1324.1324.1324.1324.1324.1324.1324.1325.1326.1326.1326.1326.1326.1326.1326.1326.1350.1354.1354.1354.1354.1356.1356.1356.1356.1356.1356.1356.1356.1356.1357.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1368.1368.1368.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1375.1378.1378.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1388.1388.1388.1394.1394.1394.1394.1394.1394.1394.1394.1394.1410.1416.1417.1417.1417.1417.1417.1417.1417.1417.1417.1417.1417.1417.1418.1420.1420.1420.1420.1420.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1424.1426.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: 58 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. 55. 56. 57. 58.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 1m8.502s user 0m44.952s sys 0m2.453s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 1m8.978s user 0m54.510s sys 0m2.565s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 1m39.261s user 1m7.610s sys 0m1.005s Atomic solvent excluded volume calculations underway FORTRAN STOP real 27m31.461s user 27m29.286s sys 0m0.312s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASH 125 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 End of MakeDOCK sphere and grid generation.