Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-11.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 84: No such file or directory. bzcat: Can't open input file 23: 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 84: No such file or directory. bzcat: Can't open input file 23: 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 0m1.761s user 0m0.242s 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 0:1496 spheres. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 98. 101. 103. 103. 103. 106. 163. 163. 193. 193. 193. 194. 194. 194. 194. 194. 194. 194. 194. 194. 196. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 200. 200. 200. 200. 200. 200. 200. 200. 200. 200. 200. 200. 200. 204. 204. 204. 204. 205. 205. 205. 205. 205. 205. 205. 205. 205. 205. 205. 205. 205. 205. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 208. 208. 208. 208. 208. 208. 208. 208. 208. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 211. 211. 211. 211. 211. 214. 214. 214. 214. 214. 214. 214. 215. 215. 215. 215. 215. 215. 215. 215. 216. 216. 216. 219. 219. 219. 219. 221. 221. 221. 221. 221. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 228. 231. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 236. 236. 236. 236. 236. 236. 236. 236. 236. 237. 293. 293. 296. 296. 296. 297. 297. 297. 298. 298. 298. 298. 298. 298. 298. 299. 299. 299. 299. 299. 299. 299. 299. 299. 299. 299. 299. 299. 299. 299. 299. 299. 299. 299. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 301. 302. 302. 302. 302. 302. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 303. 313. 314. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 315. 327. 327. 327. 327. 327. 327. 327. 327. 327. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 329. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 330. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 331. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 347. 347. 347. 347. 347. 347. 347. 347. 347. 347. 347. 347. 347. 348. 348. 348. 348. 348. 348. 475. 478. 478. 478. 478. 478. 479. 479. 479. 479. 479. 479. 479. 479. 479. 479. 480. 480. 480. 480. 480. 480. 480. 480. 480. 480. 480. 481. 481. 481. 481. 481. 481. 481. 482. 482. 482. 482. 482. 482. 482. 482. 482. 482. 482. 482. 482. 482. 482. 482. 482. 482. 482. 482. 484. 487. 487. 487. 487. 487. 487. 487. 487. 506. 508. 508. 508. 508. 508. 508. 508. 508. 508. 508. 508. 508. 508. 508. 508. 508. 515. 515. 516. 516. 516. 516. 516. 516. 516. 516. 516. 517. 517. 517. 517. 517. 517. 517. 517. 517. 517. 517. 517. 517. 517. 519. 519. 520. 521. 521. 521. 521. 521. 521. 521. 521. 521. 521. 521. 521. 521. 521. 521. 521. 521. 521. 521. 521. 522. 525. 525. 525. 540. 540. 540. 540. 540. 540. 540. 540. 540. 540. 584. 584. 584. 584. 594. 594. 594. 594. 594. 594. 594. 594. 594. 594. 594. 594. 595. 595. 596. 596. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 598. 600. 602. 602. 603. 603. 603. 603. 603. 603. 603. 603. 603. 603. 603. 603. 603. 604. 607. 607. 611. 611. 611. 611. 611. 611. 615. 615. 615. 615. 615. 615. 615. 621. 621. 621. 621. 621. 621. 621. 621. 621. 622. 622. 622. 623. 627. 627. 627. 627. 627. 627. 635. 635. 736. 736. 749. 749. 749. 749. 749. 752. 753. 754. 754. 754. 756. 756. 769. 769. 769. 769. 769. 771. 771. 771. 771. 771. 771. 771. 771. 771. 771. 771. 771. 771. 771. 771. 771. 771. 771. 771. 775. 776. 776. 776. 778. 778. 778. 778. 778. 778. 779. 779. 779. 779. 779. 779. 779. 780. 780. 780. 780. 780. 780. 780. 780. 780. 780. 781. 781. 781. 781. 781. 781. 781. 785. 785. 785. 785. 785. 785. 785. 785. 785. 785. 785. 785. 785. 785. 785. 788. 788. 788. 788. 788. 788. 788. 788. 788. 789. 789. 789. 789. 789. 789. 789. 789. 789. 789. 789. 789. 789. 789. 790. 792. 792. 793. 793. 793. 796. 796. 797. 797. 798. 798. 798. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 799. 800. 800. 800. 800. 800. 800. 800. 800. 800. 800. 800. 800. 800. 800. 800. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 801. 803. 803. 803. 803. 804. 804. 804. 806. 806. 806. 806. 806. 806. 806. 806. 806. 806. 811. 811. 811. 811. 811. 811. 814. 814. 814. 814. 814. 814. 814. 814. 814. 814. 814. 814. 814. 814. 820. 825. 825. 827. 828. 829. 830. 830. 830. 830. 830. 830. 830. 830. 834. 835. 835. 835. 835. 836. 836. 836. 836. 836. 836. 836. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 838. 838. 838. 838. 838. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846.1148.1148.1148.1148.1148.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1155.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1170.1170.1170.1170.1170.1170.1181.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1188.1188.1188.1188.1188.1193.1194.1194.1194.1194.1196.1196.1196.1196.1196.1199.1199.1199.1199.1199.1199.1199.1201.1201.1201.1201.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1205.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1206.1207.1207.1207.1207.1207.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1208.1227.1227.1227.1227.1227.1227.1227.1227.1229.1229.1229.1229.1229.1229.1229.1229.1231.1231.1231.1231.1231.1231.1231.1231.1231.1231.1231.1231.1231.1232.1234.1235.1235.1235.1235.1235.1235.1235.1235.1235.1235.1245.1245.1247.1247.1247.1247.1247.1247.1247.1247.1247.1247.1247.1247.1247.1247.1248.1248.1248.1248.1248.1248.1248.1248.1248.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1264.1264.1265.1265.1265.1265.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1266.1267.1267.1267.1268.1269.1269.1269.1269.1269.1269.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1271.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1275.1275.1275.1275.1275.1275.1275.1275.1275.1275.1276.1276.1276.1276.1276.1276.1276.1276.1276.1276.1276.1276.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1281.2115.2115.2116.2118.2118.2119.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2120.2121.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: 28 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.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 0m27.904s user 0m25.364s sys 0m0.671s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m29.158s user 0m23.748s sys 0m0.601s Creating box around spheres Creating chemgrid maps real 0m11.275s user 0m9.949s sys 0m0.209s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m15.441s user 18m14.984s sys 0m0.070s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASN 14 has a net charge of -0.2720 !!! WARNING: GLY 31 has a net charge of -0.2720 !!! WARNING: GLY 170 has a net charge of -0.2720 !!! WARNING: LEU 353 has a net charge of -0.2720 !!! WARNING: ASN 14 has a net charge of -0.2720 !!! WARNING: GLY 31 has a net charge of -0.2720 !!! WARNING: GLY 170 has a net charge of -0.2720 !!! WARNING: LEU 353 has a net charge of -0.2720 !!! WARNING: ASN 14 has a net charge of -0.2720 !!! WARNING: GLY 31 has a net charge of -0.2720 !!! WARNING: GLY 170 has a net charge of -0.2720 !!! WARNING: LEU 353 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