Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-21.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 0m17.811s user 0m0.198s sys 0m0.133s 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 0:1369 spheres. 55. 57. 58. 59. 59. 59. 59. 60. 60. 60. 60. 60. 60. 60. 60. 60. 60. 60. 60. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 61. 66. 66. 66. 66. 66. 66. 66. 66. 67. 69. 69. 71. 71. 71. 71. 71. 71. 71. 71. 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. 73. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 76. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 85. 85. 85. 85. 85. 85. 85. 85. 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. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 172. 172. 183. 183. 197. 197. 197. 199. 199. 199. 199. 199. 199. 199. 199. 203. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 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624. 624. 624. 624. 624. 625. 625. 625. 625. 625. 625. 625. 625. 625. 626. 626. 633. 641. 641. 641. 641. 641. 641. 641. 656. 662. 662. 662. 662. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 666. 666. 666. 666. 666. 668. 669. 669. 669. 669. 669. 669. 669. 669. 669. 669. 670. 670. 670. 670. 670. 822. 822. 822. 822. 822. 825. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 831. 831. 831. 831. 831. 840. 840. 840. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 939. 939. 953. 955. 955. 955. 955. 955. 955. 955. 955. 955. 955. 955. 965. 965. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 966. 968. 968. 968. 968. 968. 968. 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987.1000.1000.1000.1000.1000.1006.1006.1006.1006.1011.1011.1011.1011.1013.1014.1014.1014.1014.1014.1014.1014.1014.1015.1015.1015.1017.1018.1018.1018.1018.1108.1108.1108.1108.1109.1109.1109.1109.1109.1109.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1114.1114.1114.1115.1116.1117.1117.1117.1118.1118.1118.1118.1118.1118.1118.1118.1118.1120.1120.1123.1123.1123.1123.1123.1123.1126.1126.1126.1126.1126.1126.1127.1127.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1134.1135.1140.1140.1140.1140.1140.1140.1141.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1143.1143.1143.1143.1143.1143.1145.1145.1146.1146.1146.1148.1148.1148.1148.1148.1148.1148.1153.1153.1154.1154.1154.1154.1154.1154.1154.1154.1156.1156.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1163.1163.1163.1168.1168.1168.1168.1168.1168.1181.1181.1181.1182.1182.1321.1325.1325.1325.1325.1325.1325.1326.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1346.1346.1346.1346.1346.1346.1346.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1358.1359.1359.1359.1360.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1374.1374.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1387.1387.1387.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1397.1397.1397.1397.1397.1397.1397.1397.1412.1412.1418.1418.1419.1419.1419.1419.1419.1419.1419.1419.1419.1419.1419.1420.1422.1422.1422.1422.1424.1424.1424.1424.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1426.1426.1426.1426.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: 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 1m41.988s user 0m25.032s sys 0m0.691s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m41.436s user 0m24.668s sys 0m0.683s Creating box around spheres Creating chemgrid maps real 0m38.832s user 0m10.222s sys 0m0.252s Atomic solvent excluded volume calculations underway FORTRAN STOP real 55m0.444s user 18m48.197s sys 0m0.370s 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.