Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-10.c.bkslab.org du2 starts 1 molecule processed, 0 errors first try already in then inzinc count is 0 nothing to compress count is 0 nothing to compress nothing to compress nothing to compress du2.csh script updated ligand processing 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 0m27.080s user 0m0.221s sys 0m0.112s 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 0:1531 spheres. 66. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 70. 70. 70. 70. 70. 70. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 73. 74. 74. 81. 81. 82. 82. 82. 85. 85. 86. 86. 86. 86. 181. 181. 181. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 195. 195. 195. 195. 195. 195. 195. 195. 196. 196. 196. 196. 196. 196. 196. 196. 196. 196. 196. 207. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 213. 213. 213. 213. 213. 217. 217. 218. 218. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 222. 223. 223. 223. 225. 226. 226. 226. 226. 226. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 229. 229. 229. 229. 229. 229. 229. 229. 229. 230. 230. 230. 242. 242. 242. 242. 242. 242. 358. 358. 359. 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639. 639. 639. 639. 639. 654. 654. 654. 660. 660. 660. 660. 660. 661. 661. 661. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 664. 664. 664. 664. 664. 664. 667. 667. 667. 667. 667. 667. 668. 668. 668. 668. 668. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 670. 820. 820. 820. 820. 820. 820. 822. 823. 823. 824. 824. 824. 824. 824. 824. 825. 825. 825. 825. 827. 827. 827. 827. 827. 827. 836. 836. 836. 836. 839. 839. 839. 839. 839. 839. 840. 935. 935. 935. 949. 951. 951. 951. 951. 951. 951. 951. 951. 951. 951. 960. 960. 961. 961. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 964. 964. 964. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 971. 973. 973. 973. 973. 973. 973. 973. 973. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 980. 980. 980. 980. 980. 980. 981. 981. 981. 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990.1003.1003.1003.1003.1003.1003.1003.1003.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1010.1011.1011.1011.1011.1011.1011.1011.1011.1011.1011.1012.1013.1013.1013.1013.1013.1014.1014.1014.1093.1093.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1095.1099.1100.1100.1100.1101.1101.1101.1101.1102.1102.1102.1102.1102.1103.1104.1104.1104.1104.1104.1104.1104.1104.1104.1105.1105.1105.1105.1105.1109.1110.1110.1110.1110.1110.1110.1110.1110.1111.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1112.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1116.1116.1116.1119.1119.1119.1119.1119.1119.1121.1121.1121.1121.1121.1121.1121.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1124.1125.1125.1125.1125.1125.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1135.1135.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1137.1137.1138.1138.1139.1140.1140.1140.1141.1141.1141.1141.1141.1141.1142.1142.1142.1142.1142.1142.1142.1142.1142.1144.1144.1144.1144.1144.1144.1144.1144.1149.1149.1149.1150.1150.1150.1150.1150.1150.1150.1153.1153.1153.1154.1154.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1164.1164.1164.1164.1166.1166.1166.1166.1168.1170.1170.1170.1170.1170.1170.1170.1170.1170.1170.1170.1170.1170.1170.1171.1171.1171.1171.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1173.1173.1173.1173.1173.1173.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1177.1178.1178.1200.1200.1200.1200.1200.1214.1214.1214.1214.1214.1214.1214.1217.1217.1217.1217.1218.1218.1218.1218.1218.1317.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1321.1322.1323.1323.1323.1323.1323.1323.1323.1323.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1338.1338.1338.1338.1353.1353.1353.1354.1354.1354.1354.1354.1354.1354.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1356.1356.1356.1365.1365.1365.1365.1366.1366.1366.1366.1366.1367.1367.1367.1367.1367.1367.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1372.1372.1372.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1383.1385.1385.1385.1385.1385.1385.1385.1385.1392.1392.1392.1392.1392.1392.1392.1392.1392.1393.1393.1393.1393.1393.1393.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1415.1415.1415.1415.1415.1415.1415.1418.1418.1418.1418.1418.1420.1420.1420.1420.1420.1420.1420.1420.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1422.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: 59 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. 59.FORTRAN STOP Adding essential hydrogens to receptor #@jens_hydrogens.csh rec.pdb 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 1m48.325s user 0m27.363s sys 0m0.832s Adding spheres to tarted electrostatic grid we had to cook * NE2* we had to cook *HNE2* we had to cook *HNE1* Creating DelPhi electrostatic grid real 1m33.981s user 0m26.069s sys 0m0.771s Creating box around spheres Creating chemgrid maps real 0m36.488s user 0m9.892s sys 0m0.301s Atomic solvent excluded volume calculations underway FORTRAN STOP real 46m40.518s user 17m40.967s sys 0m0.060s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. Stop before docking.