Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-13.c.bkslab.org du2 starts 1 molecule processed, 0 errors first try already in then inzinc count is 0 bzcat: Can't open input file 21: No such file or directory. bzcat: Can't open input file 77: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. count is 0 bzcat: Can't open input file 17: No such file or directory. bzcat: Can't open input file 94: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. bzcat: Can't open input file 21: No such file or directory. bzcat: Can't open input file 77: No such file or directory. bzcat: Can't open input file 17: No such file or directory. bzcat: Can't open input file 94: No such file or directory. 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 0m35.993s user 0m0.199s sys 0m0.115s 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 0:1536 spheres. 66. 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. 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. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 76. 76. 76. 76. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 180. 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. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 197. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 212. 212. 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616. 616. 617. 617. 617. 617. 617. 617. 617. 617. 618. 618. 618. 618. 620. 620. 620. 620. 620. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 624. 629. 629. 629. 629. 631. 631. 631. 631. 631. 631. 639. 639. 639. 639. 639. 639. 654. 654. 660. 660. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 664. 664. 664. 664. 664. 664. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 668. 668. 668. 668. 668. 668. 670. 670. 820. 820. 820. 820. 820. 820. 820. 820. 820. 820. 820. 822. 823. 823. 823. 823. 823. 824. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 829. 829. 829. 829. 830. 838. 838. 838. 838. 838. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 841. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 934. 934. 934. 937. 937. 937. 937. 937. 937. 937. 937. 937. 937. 937. 937. 937. 937. 937. 951. 951. 951. 951. 953. 953. 953. 953. 953. 953. 953. 963. 963. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 966. 966. 966. 966. 966. 966. 966. 966. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 973. 974. 974. 974. 974. 974. 975. 975. 975. 975. 975. 975. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 977. 980. 980. 980. 982. 982. 982. 982. 982. 983. 984. 984. 984. 984. 984. 984. 984. 984. 984. 984. 984. 984. 985. 998. 998. 998. 998. 998. 998. 998. 998. 998.1006.1006.1006.1006.1006.1006.1009.1009.1009.1009.1009.1012.1012.1012.1012.1012.1012.1012.1012.1012.1013.1013.1015.1015.1016.1016.1016.1016.1101.1101.1101.1101.1101.1101.1101.1101.1101.1101.1102.1102.1106.1106.1106.1107.1107.1107.1107.1107.1107.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1109.1112.1112.1112.1112.1112.1112.1114.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1118.1118.1118.1121.1121.1121.1121.1121.1121.1124.1124.1124.1124.1125.1125.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1132.1137.1138.1138.1138.1139.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1141.1141.1141.1141.1143.1143.1143.1143.1144.1144.1144.1144.1145.1145.1146.1146.1146.1146.1146.1146.1146.1146.1146.1152.1152.1152.1152.1153.1153.1153.1154.1154.1154.1154.1155.1155.1155.1156.1156.1156.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1161.1162.1162.1162.1166.1166.1166.1166.1178.1319.1323.1323.1323.1323.1323.1323.1323.1323.1323.1324.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1344.1344.1344.1344.1344.1344.1344.1344.1344.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1355.1355.1355.1356.1356.1356.1356.1356.1357.1357.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1369.1369.1369.1369.1369.1369.1369.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1381.1385.1385.1385.1385.1385.1385.1385.1385.1385.1393.1393.1393.1393.1393.1393.1393.1393.1408.1408.1415.1415.1415.1415.1415.1415.1415.1415.1415.1415.1415.1418.1418.1418.1418.1418.1420.1420.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1422.1422.1422.1422.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: 45 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.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 1m49.498s user 0m27.495s sys 0m0.782s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m51.647s user 0m27.456s sys 0m0.868s Creating box around spheres Creating chemgrid maps real 0m36.629s user 0m10.792s sys 0m0.316s Atomic solvent excluded volume calculations underway FORTRAN STOP real 57m39.808s user 19m0.254s sys 0m0.089s 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.