Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-29.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 65: No such file or directory. bzcat: Can't open input file 58: 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 65: No such file or directory. bzcat: Can't open input file 58: 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 1m19.626s user 0m0.216s sys 0m0.115s 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 0:1236 spheres. 66. 66. 66. 66. 72. 72. 72. 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. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 84. 84. 84. 84. 86. 86. 86. 86. 87. 87. 87. 88. 88. 88. 88. 88. 88. 185. 199. 199. 199. 199. 201. 201. 201. 201. 201. 201. 201. 201. 201. 201. 201. 201. 201. 211. 211. 211. 211. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 214. 214. 214. 214. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 217. 221. 221. 222. 222. 222. 223. 223. 224. 225. 230. 230. 230. 230. 230. 230. 231. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 233. 233. 233. 233. 233. 233. 240. 240. 240. 240. 240. 240. 240. 246. 246. 246. 254. 254. 254. 254. 254. 254. 254. 254. 254. 254. 254. 254. 254. 254. 257. 257. 257. 257. 257. 260. 260. 260. 260. 261. 261. 263. 263. 263. 264. 264. 264. 264. 357. 360. 360. 360. 360. 361. 361. 361. 361. 361. 361. 361. 361. 361. 363. 363. 363. 363. 363. 363. 364. 369. 369. 371. 371. 371. 371. 371. 371. 371. 371. 372. 372. 372. 373. 374. 375. 375. 375. 375. 375. 375. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 379. 379. 379. 379. 379. 379. 379. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 384. 384. 384. 384. 384. 384. 384. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 387. 387. 387. 391. 391. 392. 392. 392. 392. 394. 394. 394. 394. 399. 400. 400. 401. 401. 401. 401. 403. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 406. 406. 406. 406. 406. 406. 406. 406. 406. 406. 406. 406. 406. 406. 406. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 409. 414. 414. 414. 426. 587. 587. 587. 587. 587. 600. 600. 600. 600. 600. 600. 600. 602. 602. 602. 602. 602. 603. 603. 603. 603. 603. 603. 603. 603. 603. 604. 605. 605. 605. 611. 611. 615. 616. 616. 616. 616. 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. 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. 624. 624. 624. 624. 624. 625. 625. 625. 625. 625. 625. 625. 625. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 634. 634. 634. 634. 634. 634. 634. 634. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 641. 641. 641. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 657. 657. 657. 657. 657. 659. 661. 663. 663. 663. 663. 664. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 667. 667. 667. 667. 667. 669. 669. 669. 669. 669. 669. 669. 669. 670. 670. 670. 670. 670. 671. 671. 671. 671. 671. 673. 673. 673. 673. 824. 826. 827. 830. 830. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 833. 833. 834. 834. 834. 834. 834. 842. 842. 842. 842. 842. 842. 842. 842. 844. 844. 845. 845. 845. 845. 845. 845. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 942. 942. 942. 942. 942. 950. 950. 950. 950. 950. 950. 950. 950. 959. 959. 959. 959. 959. 959. 959. 959. 969. 969. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 972. 972. 972. 972. 972. 972. 972. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 979. 979. 979. 980. 980. 980. 980. 980. 980. 980. 981. 981. 983. 983. 983. 983. 983. 983. 983. 984. 988. 988. 988. 988. 989. 989. 989. 990. 990. 991. 991. 991.1005.1005.1005.1005.1005.1005.1005.1012.1012.1107.1107.1108.1113.1113.1114.1114.1114.1118.1118.1118.1121.1121.1121.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1138.1138.1138.1138.1144.1144.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1147.1147.1148.1149.1149.1149.1149.1150.1150.1150.1152.1152.1152.1152.1152.1152.1157.1157.1157.1158.1158.1158.1158.1158.1158.1159.1160.1160.1161.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1163.1164.1164.1164.1164.1164.1164.1164.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1167.1167.1167.1167.1167.1170.1172.1172.1172.1172.1172.1172.1172.1172.1184.1184.1184.1184.1184.1184.1204.1207.1207.1207.1207.1207.1207.1207.1208.1208.1208.1208.1208.1208.1208.1209.1209.1209.1209.1209.1209.1329.1329.1329.1329.1329.1329.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1330.1345.1358.1358.1358.1358.1358.1360.1360.1360.1360.1360.1361.1361.1361.1362.1362.1362.1362.1362.1363.1363.1367.1367.1367.1367.1367.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1379.1379.1382.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1385.1385.1388.1388.1388.1392.1392.1392.1392.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1407.1407.1407.1407.1407.1407.1407.1407.1407.1407.1415.1415.1415.1415.1415.1415.1415.1421.1421.1421.1421.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1425.1425.1425.1425.1425.1425.1427.1427.1427.1427.1428.1428.1428.1428.1428.1428.1428.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: 39 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.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 1m51.700s user 0m26.326s sys 0m0.777s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m42.614s user 0m27.407s sys 0m0.841s Creating box around spheres Creating chemgrid maps real 0m36.509s user 0m10.462s sys 0m0.277s Atomic solvent excluded volume calculations underway FORTRAN STOP real 55m41.487s user 18m48.978s sys 0m0.267s 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.