Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-1-31.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 51: No such file or directory. bzcat: Can't open input file 92: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. count is 0 nothing to compress bzcat: Can't open input file 51: No such file or directory. bzcat: Can't open input file 92: No such file or directory. 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 0m2.845s user 0m0.527s sys 0m0.423s 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 0:1665 spheres. 130. 130. 130. 130. 131. 131. 131. 131. 131. 131. 131. 131. 131. 131. 131. 131. 131. 131. 131. 131. 131. 131. 225. 225. 225. 225. 225. 225. 225. 225. 225. 225. 225. 225. 226. 229. 229. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 236. 237. 237. 237. 237. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 240. 240. 240. 240. 242. 242. 242. 242. 242. 242. 242. 242. 243. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 246. 249. 249. 249. 249. 249. 249. 250. 250. 250. 250. 250. 250. 250. 250. 251. 251. 251. 251. 251. 251. 251. 251. 252. 252. 252. 252. 252. 252. 252. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 258. 259. 259. 259. 259. 259. 259. 259. 259. 259. 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554. 554. 554. 554. 554. 555. 556. 578. 578. 578. 580. 580. 580. 580. 580. 580. 580. 580. 587. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 589. 589. 589. 589. 589. 589. 589. 589. 589. 589. 589. 589. 589. 591. 591. 591. 591. 591. 591. 592. 592. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 594. 597. 597. 597. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 656. 656. 656. 656. 656. 656. 656. 656. 666. 668. 668. 669. 669. 669. 669. 669. 669. 669. 669. 669. 670. 672. 672. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 676. 678. 678. 678. 683. 683. 683. 683. 683. 684. 684. 684. 684. 684. 687. 687. 687. 692. 692. 692. 692. 692. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 695. 695. 695. 699. 705. 705. 705. 705. 705. 705. 705. 707. 707. 707. 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918.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1229.1229.1229.1232.1232.1232.1233.1233.1233.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1235.1235.1235.1235.1235.1235.1235.1235.1235.1235.1235.1235.1235.1235.1235.1235.1235.1235.1237.1243.1243.1243.1243.1243.1243.1243.1243.1243.1243.1243.1243.1243.1243.1256.1256.1256.1260.1261.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1266.1266.1266.1266.1266.1267.1267.1267.1267.1267.1267.1267.1267.1267.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1268.1269.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1273.1273.1273.1273.1273.1273.1273.1275.1275.1275.1275.1275.1276.1276.1276.1276.1276.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1279.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1280.1317.1318.1318.1318.1318.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1320.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1335.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1336.1337.1337.1337.1337.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1340.1340.1340.1340.1341.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1348.1348.1348.1348.1348.1348.1351.1353.1354.1354.1354.1355.1355.2160.2160.2161.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2165.2166.2166.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: 29 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.FORTRAN STOP Adding essential hydrogens to receptor 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 0m36.494s user 0m30.124s sys 0m0.919s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m33.801s user 0m29.735s sys 0m0.880s Creating box around spheres Creating chemgrid maps real 0m45.873s user 0m45.067s sys 0m0.323s Atomic solvent excluded volume calculations underway FORTRAN STOP real 32m28.771s user 32m27.735s sys 0m0.236s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar failed to get similars