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 0m28.895s user 0m0.210s sys 0m0.124s 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 0:1398 spheres. 66. 66. 66. 66. 66. 66. 66. 66. 66. 69. 69. 69. 69. 69. 69. 71. 71. 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. 75. 75. 84. 84. 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. 183. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 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. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 219. 220. 220. 220. 221. 221. 221. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 228. 228. 228. 228. 229. 229. 229. 229. 229. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 261. 261. 261. 261. 261. 262. 262. 348. 349. 349. 350. 350. 350. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 358. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 362. 367. 367. 367. 367. 367. 367. 367. 367. 368. 368. 370. 370. 370. 370. 370. 370. 370. 370. 371. 372. 372. 372. 372. 373. 373. 373. 373. 373. 373. 373. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 378. 382. 382. 382. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 389. 389. 390. 390. 390. 390. 390. 390. 392. 392. 392. 392. 392. 392. 392. 398. 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617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 633. 633. 633. 633. 633. 633. 633. 633. 633. 639. 639. 639. 639. 639. 639. 640. 640. 640. 640. 640. 640. 640. 640. 640. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 656. 661. 662. 662. 663. 663. 663. 663. 663. 663. 663. 663. 663. 663. 664. 664. 666. 666. 666. 666. 666. 666. 669. 669. 669. 669. 669. 669. 670. 670. 670. 670. 822. 822. 822. 822. 822. 822. 823. 825. 825. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 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. 831. 831. 831. 831. 831. 831. 840. 840. 840. 840. 840. 840. 841. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 844. 844. 844. 844. 844. 844. 844. 928. 928. 939. 939. 953. 953. 955. 955. 955. 955. 955. 955. 955. 955. 965. 965. 966. 966. 966. 966. 966. 966. 966. 966. 966. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 975. 976. 976. 976. 977. 977. 977. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 982. 983. 984. 984. 984. 984. 984. 984. 984. 984. 985. 985. 985. 985. 985. 985. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 986. 987. 987. 987. 987. 987. 987. 987. 999.1000.1000.1000.1011.1014.1014.1014.1014.1014.1014.1014.1014.1014.1015.1015.1017.1018.1104.1105.1109.1109.1109.1109.1109.1109.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1114.1114.1114.1114.1115.1115.1116.1118.1118.1118.1118.1118.1118.1120.1123.1123.1123.1123.1123.1123.1123.1126.1126.1126.1126.1126.1126.1126.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1134.1135.1136.1136.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1142.1142.1142.1142.1142.1142.1142.1143.1144.1144.1144.1145.1146.1146.1147.1148.1148.1148.1148.1148.1148.1148.1153.1153.1154.1154.1154.1154.1154.1154.1154.1154.1157.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1163.1163.1163.1163.1164.1164.1168.1168.1168.1168.1168.1168.1168.1168.1321.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1355.1355.1355.1355.1355.1355.1355.1355.1355.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1359.1369.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1382.1397.1397.1397.1397.1412.1418.1418.1418.1419.1419.1419.1419.1419.1419.1419.1419.1419.1419.1419.1419.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1426.1426.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 1m48.252s user 0m25.937s sys 0m0.822s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m51.155s user 0m26.667s sys 0m0.851s Creating box around spheres Creating chemgrid maps real 0m36.903s user 0m10.912s sys 0m0.294s Atomic solvent excluded volume calculations underway FORTRAN STOP real 56m25.000s user 18m53.125s sys 0m0.171s 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.