Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-13.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 49: No such file or directory. bzcat: Can't open input file 29: 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 49: No such file or directory. bzcat: Can't open input file 29: 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 0m58.657s user 0m0.242s sys 0m0.100s 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 0:1333 spheres. 63. 63. 66. 67. 67. 67. 68. 69. 69. 69. 69. 71. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 73. 73. 73. 73. 73. 73. 73. 75. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 172. 181. 182. 197. 199. 209. 209. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 219. 219. 221. 221. 221. 221. 221. 221. 222. 222. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 224. 228. 228. 228. 228. 228. 228. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 235. 235. 244. 244. 244. 244. 244. 244. 244. 244. 244. 250. 253. 253. 253. 253. 253. 256. 256. 258. 258. 258. 258. 258. 258. 258. 258. 260. 260. 261. 261. 261. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 349. 349. 349. 349. 349. 351. 351. 351. 351. 351. 351. 351. 355. 355. 355. 356. 360. 360. 360. 362. 362. 362. 362. 362. 363. 363. 363. 363. 363. 363. 363. 363. 363. 363. 363. 363. 363. 363. 363. 363. 363. 363. 363. 363. 364. 364. 364. 364. 364. 364. 364. 370. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 371. 372. 372. 372. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 375. 375. 375. 375. 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. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 379. 379. 379. 379. 380. 380. 380. 380. 380. 384. 386. 386. 386. 386. 386. 386. 386. 387. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 394. 394. 394. 394. 394. 396. 400. 400. 400. 400. 400. 401. 401. 401. 401. 401. 401. 404. 404. 404. 404. 404. 404. 404. 404. 404. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 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. 409. 414. 414. 414. 427. 587. 587. 587. 587. 587. 587. 587. 587. 587. 587. 587. 587. 587. 588. 588. 602. 602. 602. 602. 602. 602. 602. 602. 604. 604. 605. 605. 605. 605. 605. 605. 605. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 611. 616. 618. 618. 618. 618. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 621. 621. 621. 621. 621. 621. 623. 623. 623. 623. 623. 623. 623. 623. 624. 626. 626. 626. 626. 626. 626. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 629. 629. 629. 634. 634. 634. 634. 634. 635. 635. 635. 635. 635. 635. 636. 636. 636. 636. 636. 636. 636. 636. 636. 636. 636. 636. 636. 636. 644. 644. 644. 644. 644. 644. 644. 644. 644. 659. 659. 659. 665. 665. 666. 666. 666. 666. 666. 666. 666. 666. 666. 667. 667. 669. 669. 669. 671. 672. 672. 673. 673. 673. 673. 673. 673. 673. 673. 673. 829. 829. 829. 829. 829. 829. 831. 831. 831. 831. 831. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 832. 833. 833. 833. 833. 833. 833. 833. 833. 833. 835. 835. 844. 844. 844. 846. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 848. 848. 848. 848. 848. 848. 848. 848. 848. 848. 848. 848. 848. 848. 848. 848. 848. 848. 936. 942. 942. 942. 942. 959. 959. 959. 959. 959. 959. 959. 963. 969. 969. 969. 969. 969. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 972. 972. 972. 972. 972. 972. 972. 972. 972. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 976. 980. 980. 980. 980. 980. 980. 980. 980. 981. 981. 981. 981. 981. 981. 982. 983. 983. 983. 983. 983. 983. 983. 983. 983. 983. 983. 983. 983. 983. 983. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 988. 989. 989. 990. 990. 990. 990. 990. 990. 990. 990. 990. 991. 991. 991. 991. 991. 991.1004.1004.1004.1004.1004.1004.1004.1004.1010.1012.1012.1012.1108.1108.1108.1108.1108.1108.1108.1115.1115.1115.1116.1116.1116.1116.1116.1120.1122.1122.1122.1124.1124.1124.1124.1124.1126.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1133.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1139.1139.1140.1140.1140.1140.1140.1140.1142.1142.1146.1146.1146.1146.1146.1146.1146.1146.1146.1147.1147.1147.1147.1147.1149.1149.1150.1151.1151.1151.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1154.1154.1154.1154.1159.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1163.1163.1163.1163.1163.1165.1165.1165.1165.1165.1165.1167.1167.1167.1167.1167.1169.1174.1174.1174.1180.1180.1180.1180.1180.1180.1180.1180.1180.1181.1182.1182.1182.1182.1182.1182.1184.1184.1188.1188.1347.1347.1349.1349.1363.1364.1364.1365.1365.1365.1365.1365.1365.1365.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1381.1381.1383.1386.1386.1386.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1388.1388.1388.1388.1388.1388.1388.1388.1388.1389.1394.1394.1395.1395.1395.1396.1396.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1419.1419.1419.1419.1420.1420.1421.1425.1425.1425.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1427.1427.1429.1429.1429.1431.1432.1432.1432.1432.1432.1432.1435.1435.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: 54 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. 40. 41. 42. 43. 44. 45. 46. 47. 48. 49. 50. 51. 52. 53. 54.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 1m20.799s user 0m21.064s sys 0m0.604s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m10.025s user 0m20.445s sys 0m0.580s Creating box around spheres Creating chemgrid maps real 0m38.524s user 0m14.941s sys 0m0.218s Atomic solvent excluded volume calculations underway FORTRAN STOP real 78m45.788s user 28m35.458s sys 0m0.192s 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.