Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-20.c.bkslab.org du2 starts 1 molecule processed, 0 errors convert.py (MDL SDF -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. mol2nam v1.9 Structure to Name Conversion OpenEye Scientific Software, February 2009 convert.py (Tripos MOL2 -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. mid: No such file or directory. hi: No such file or directory. lo: No such file or directory. mid: No such file or directory. first try already in then inzinc count is 0 bzcat: Can't open input file 45: No such file or directory. bzcat: Can't open input file 06: 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 45: No such file or directory. bzcat: Can't open input file 28: 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 45: No such file or directory. bzcat: Can't open input file 06: No such file or directory. bzcat: Can't open input file 45: No such file or directory. bzcat: Can't open input file 28: No such file or directory. 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 0m2.871s user 0m0.236s sys 0m0.316s 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 0:1472 spheres. 130. 130. 130. 130. 130. 130. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 138. 193. 193. 195. 195. 195. 225. 225. 225. 225. 225. 225. 225. 225. 226. 226. 226. 226. 226. 226. 226. 226. 226. 228. 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. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 237. 237. 237. 237. 237. 237. 237. 237. 237. 237. 237. 237. 239. 239. 239. 239. 239. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 241. 241. 241. 242. 242. 242. 242. 242. 242. 242. 242. 242. 242. 243. 243. 243. 243. 243. 244. 244. 248. 248. 248. 249. 249. 249. 249. 249. 249. 250. 250. 250. 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299. 299. 299. 301. 301. 301. 302. 302. 302. 302. 302. 302. 362. 362. 362. 362. 363. 363. 363. 365. 365. 365. 365. 365. 365. 365. 365. 365. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 369. 379. 379. 379. 379. 380. 380. 380. 381. 381. 381. 381. 381. 381. 381. 381. 381. 381. 381. 393. 393. 393. 393. 393. 393. 393. 393. 393. 396. 396. 396. 396. 396. 396. 396. 396. 396. 396. 396. 396. 396. 396. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 401. 403. 405. 405. 405. 410. 411. 411. 411. 411. 413. 413. 413. 413. 413. 413. 413. 414. 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. 552. 552. 552. 552. 552. 553. 553. 553. 553. 553. 553. 553. 553. 553. 553. 554. 554. 554. 554. 554. 554. 554. 554. 554. 554. 556. 559. 559. 559. 559. 559. 559. 559. 559. 578. 581. 581. 581. 581. 581. 581. 587. 587. 588. 588. 588. 588. 588. 588. 588. 589. 589. 589. 589. 589. 589. 589. 589. 589. 589. 589. 589. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 593. 594. 594. 597. 597. 597. 611. 611. 611. 611. 611. 611. 612. 612. 612. 612. 612. 612. 612. 612. 612. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 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. 669. 669. 669. 669. 669. 670. 670. 670. 670. 675. 675. 675. 675. 675. 675. 675. 675. 675. 675. 676. 679. 679. 679. 679. 683. 683. 683. 683. 683. 683. 683. 683. 683. 684. 684. 684. 684. 684. 684. 684. 684. 687. 687. 693. 694. 694. 694. 694. 694. 694. 694. 695. 707. 707. 803. 808. 808. 821. 821. 821. 821. 824. 824. 826. 826. 826. 826. 826. 826. 826. 828. 828. 829. 829. 832. 835. 841. 841. 841. 841. 841. 842. 843. 843. 843. 843. 843. 843. 843. 843. 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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: 25 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.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 0m26.204s user 0m23.218s sys 0m0.563s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m27.030s user 0m23.178s sys 0m0.596s Creating box around spheres Creating chemgrid maps real 0m10.820s user 0m10.259s sys 0m0.207s Atomic solvent excluded volume calculations underway FORTRAN STOP real 17m37.318s user 17m36.635s sys 0m0.096s 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