Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-14.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 98: No such file or directory. bzcat: Can't open input file 51: 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 50: No such file or directory. bzcat: Can't open input file 54: 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 98: No such file or directory. bzcat: Can't open input file 51: No such file or directory. bzcat: Can't open input file 50: No such file or directory. bzcat: Can't open input file 54: 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 0m28.790s user 0m0.256s sys 0m0.088s 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 0:1273 spheres. 63. 66. 66. 66. 66. 66. 66. 66. 66. 66. 67. 69. 69. 69. 69. 69. 69. 69. 69. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 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. 75. 75. 75. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 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. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 183. 183. 183. 183. 183. 197. 199. 199. 199. 199. 199. 199. 199. 199. 209. 210. 210. 210. 210. 210. 210. 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. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 219. 219. 220. 220. 220. 220. 221. 221. 221. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 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384. 384. 384. 384. 384. 390. 390. 390. 390. 391. 391. 391. 393. 393. 393. 393. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 396. 396. 397. 397. 397. 397. 397. 397. 397. 402. 402. 402. 402. 402. 402. 404. 404. 404. 404. 404. 404. 404. 416. 416. 416. 416. 416. 416. 593. 593. 594. 594. 594. 594. 594. 594. 594. 595. 595. 595. 595. 596. 596. 596. 596. 596. 596. 596. 596. 597. 597. 607. 607. 608. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 609. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 610. 611. 613. 616. 616. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 619. 619. 619. 619. 622. 622. 624. 624. 625. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 649. 649. 649. 655. 655. 655. 655. 655. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 657. 657. 659. 659. 659. 659. 659. 659. 662. 662. 662. 662. 662. 662. 665. 665. 818. 819. 821. 821. 821. 821. 821. 821. 821. 821. 821. 821. 822. 822. 822. 822. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 825. 825. 826. 834. 834. 834. 834. 834. 834. 836. 836. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 838. 932. 932. 932. 932. 936. 941. 941. 941. 941. 941. 941. 941. 941. 941. 941. 941. 941. 941. 941. 941. 947. 956. 956. 956. 956. 956. 956. 956. 956. 956. 956. 956. 958. 959. 959. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 962. 962. 962. 962. 962. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 966. 969. 969. 970. 971. 971. 971. 971. 971. 971. 972. 972. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 976. 977. 977. 977. 977. 977. 978. 978. 978. 978. 979. 979. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 981. 981. 986. 986. 986. 986. 986. 993. 993. 993. 993.1001.1001.1001.1001.1001.1001.1001.1001.1001.1001.1001.1001.1001.1001.1001.1001.1001.1001.1001.1001.1094.1094.1095.1095.1095.1096.1096.1096.1096.1096.1096.1096.1103.1103.1109.1109.1109.1109.1109.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1113.1114.1114.1114.1114.1114.1114.1114.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1119.1119.1119.1121.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1127.1127.1127.1127.1127.1127.1128.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1131.1132.1132.1132.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1140.1140.1140.1140.1141.1143.1143.1143.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1147.1147.1149.1149.1152.1152.1152.1152.1154.1154.1154.1154.1154.1154.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1329.1329.1329.1329.1329.1344.1344.1344.1344.1345.1345.1345.1345.1346.1346.1346.1346.1346.1346.1346.1351.1358.1358.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1361.1361.1363.1363.1366.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1368.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1399.1405.1406.1406.1406.1406.1406.1406.1406.1406.1406.1409.1409.1409.1409.1409.1411.1412.1412.1412.1412.1412.1412.1412.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: 39 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.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 1m37.405s user 0m21.891s sys 0m0.583s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m38.732s user 0m21.427s sys 0m0.566s Creating box around spheres Creating chemgrid maps real 0m49.964s user 0m14.355s sys 0m0.194s Atomic solvent excluded volume calculations underway FORTRAN STOP real 80m20.719s user 26m51.680s sys 0m0.130s 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.