Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-16.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 80: No such file or directory. bzcat: Can't open input file 86: 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 80: No such file or directory. bzcat: Can't open input file 86: No such file or directory. nothing to compress du2.csh script updated ligand processing Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 147, in ? result = server.decoys(data) File "/usr/lib64/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib64/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib64/python2.4/xmlrpclib.py", line 1147, in request return self._parse_response(h.getfile(), sock) File "/usr/lib64/python2.4/xmlrpclib.py", line 1286, in _parse_response return u.close() File "/usr/lib64/python2.4/xmlrpclib.py", line 744, in close raise Fault(**self._stack[0]) xmlrpclib.Fault: 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 0m3.716s user 0m0.249s sys 0m0.991s 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 0:2006 spheres. 130. 131. 131. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 138. 225. 225. 225. 225. 225. 225. 225. 225. 225. 225. 225. 226. 226. 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. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 237. 237. 237. 237. 237. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 239. 240. 240. 240. 240. 240. 240. 240. 240. 242. 242. 242. 242. 242. 242. 243. 243. 243. 248. 248. 248. 248. 249. 249. 249. 249. 250. 250. 250. 250. 250. 250. 274. 274. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 281. 281. 281. 281. 281. 281. 285. 285. 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521. 521. 521. 521. 521. 521. 521. 521. 521. 540. 540. 540. 540. 540. 540. 540. 540. 540. 540. 540. 540. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 541. 542. 542. 542. 542. 542. 542. 542. 543. 543. 543. 543. 543. 543. 543. 543. 543. 543. 543. 543. 543. 543. 543. 543. 543. 545. 545. 545. 545. 545. 545. 547. 550. 550. 550. 550. 550. 550. 550. 550. 550. 550. 550. 550. 550. 550. 550. 550. 550. 550. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 552. 552. 552. 552. 552. 552. 552. 552. 552. 552. 552. 553. 553. 553. 553. 553. 554. 554. 554. 554. 556. 566. 569. 569. 569. 569. 570. 570. 570. 570. 570. 570. 572. 573. 573. 573. 573. 578. 579. 579. 579. 579. 579. 579. 579. 579. 579. 580. 580. 580. 580. 580. 581. 581. 581. 581. 581. 581. 581. 581. 581. 581. 581. 581. 581. 581. 581. 581. 581. 581. 581. 581. 587. 587. 587. 587. 587. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 588. 589. 589. 589. 589. 589. 589. 589. 589. 589. 589. 591. 593. 593. 594. 594. 594. 594. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 600. 600. 602. 605. 605. 605. 605. 605. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 607. 614. 614. 614. 614. 615. 615. 615. 615. 615. 615. 615. 618. 618. 618. 618. 618. 620. 621. 622. 622. 622. 622. 622. 622. 622. 622. 622. 622. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 626. 628. 628. 632. 632. 632. 632. 634. 652. 652. 652. 652. 658. 658. 658. 666. 666. 666. 666. 666. 666. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 669. 669. 669. 669. 669. 669. 669. 669. 669. 669. 669. 669. 669. 670. 670. 672. 672. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 676. 676. 676. 679. 679. 679. 683. 683. 683. 683. 683. 683. 683. 683. 684. 684. 684. 684. 684. 684. 687. 687. 687. 692. 695. 808. 821. 824. 824. 824. 824. 825. 826. 826. 826. 826. 832. 835. 835. 841. 841. 841. 841. 841. 841. 841. 841. 842. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 848. 848. 848. 848. 848. 849. 849. 849. 849. 849. 851. 851. 851. 851. 851. 851. 851. 851. 851. 851. 851. 851. 851. 852. 852. 852. 852. 852. 852. 852. 852. 852. 857. 857. 857. 857. 857. 857. 857. 857. 857. 857. 858. 859. 859. 859. 859. 859. 859. 860. 860. 860. 860. 860. 860. 861. 861. 861. 861. 861. 861. 861. 861. 861. 861. 861. 861. 861. 861. 861. 861. 861. 861. 861. 861. 862. 862. 863. 863. 865. 865. 865. 865. 865. 865. 865. 865. 865. 865. 865. 867. 867. 867. 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886.1121.1121.1123.1123.1123.1123.1130.1130.1130.1130.1131.1135.1135.1136.1138.1140.1149.1149.1150.1150.1150.1150.1151.1151.1151.1151.1151.1151.1156.1156.1156.1156.1156.1156.1156.1156.1157.1157.1157.1158.1158.1158.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1160.1160.1160.1160.1160.1160.1160.1160.1162.1162.1162.1167.1167.1167.1167.1167.1167.1167.1167.1167.1167.1167.1167.1169.1172.1173.1173.1174.1174.1174.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1178.1178.1178.1178.1178.1180.1180.1180.1180.1180.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1190.1190.1190.1190.1193.1193.1193.1193.1194.1194.1194.1194.1194.1194.1194.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1196.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1197.1199.1199.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1204.1204.1204.1204.1204.1204.1204.1204.1204.1204.1204.1204.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1209.1209.1209.1209.1209.1209.1209.1209.1209.1218.1218.1218.1218.1220.1220.1221.1221.1221.1221.1221.1221.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1222.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1234.1235.1235.1235.1235.1241.1241.1241.1241.1242.1243.1243.1243.1243.1254.1254.1254.1254.1254.1255.1304.1304.1304.1304.1304.1304.1306.1317.1317.1318.1318.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1320.1320.1320.1323.1327.1327.1330.1330.1333.1336.1336.1336.1336.1336.1336.1336.1336.1337.1337.1337.1337.1337.1340.1340.1340.1340.1340.1340.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1341.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1343.1343.1343.1343.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1346.1346.1346.1347.1347.1347.1347.1348.1348.1348.1348.1348.1348.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1350.1350.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1351.1352.1352.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1354.1354.1355.1355.1355.1355.1355.1355.1355.1355.1355.1356.1356.1356.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1358.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1361.1361.1361.1362.1364.1366.1366.1366.1366.1366.1366.1366.1367.1367.1367.2272.2272.2272.2272.2272.2273.2275.2275.2275.2275.2275.2275.2275.2275.2275.2275.2283.2283.2283.2283.2296.2296.2296.2297.2298.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.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: 31 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.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 0m29.647s user 0m26.132s sys 0m0.869s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m28.294s user 0m25.707s sys 0m0.824s Creating box around spheres Creating chemgrid maps real 0m14.670s user 0m13.094s sys 0m0.231s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m12.402s user 18m11.797s sys 0m0.120s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: GLN 355 has a net charge of -0.2720 !!! WARNING: GLN 355 has a net charge of -0.2720 !!! WARNING: GLN 355 has a net charge of -0.2720 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