Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-13.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 89: No such file or directory. bzcat: Can't open input file 07: 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 89: No such file or directory. bzcat: Can't open input file 07: 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 0m22.445s user 0m0.214s sys 0m0.134s 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 0:1146 spheres. 62. 62. 62. 64. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 65. 66. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 67. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 71. 71. 71. 80. 80. 83. 83. 83. 83. 83. 83. 83. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 84. 170. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 195. 195. 195. 196. 197. 197. 197. 197. 197. 197. 197. 197. 207. 207. 207. 207. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 210. 210. 210. 210. 210. 210. 210. 213. 213. 213. 213. 213. 218. 219. 219. 219. 219. 219. 219. 219. 221. 221. 221. 221. 221. 221. 221. 226. 227. 228. 228. 228. 228. 229. 229. 229. 229. 229. 236. 236. 236. 236. 236. 236. 236. 236. 243. 248. 248. 248. 248. 248. 248. 248. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 250. 347. 348. 348. 348. 348. 348. 348. 348. 348. 348. 349. 349. 350. 350. 350. 352. 352. 352. 357. 358. 358. 358. 358. 358. 358. 358. 360. 360. 360. 360. 360. 360. 360. 360. 360. 360. 360. 360. 360. 363. 363. 363. 363. 363. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 367. 367. 367. 367. 368. 368. 368. 369. 370. 371. 373. 373. 373. 373. 373. 373. 373. 374. 375. 376. 376. 376. 376. 379. 380. 380. 380. 380. 380. 380. 380. 382. 382. 382. 382. 382. 382. 382. 382. 387. 387. 388. 388. 388. 388. 388. 388. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 398. 398. 402. 416. 416. 419. 574. 574. 575. 575. 575. 588. 590. 590. 590. 590. 590. 590. 591. 591. 591. 591. 591. 591. 591. 591. 597. 597. 602. 602. 602. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 612. 612. 612. 612. 612. 613. 613. 613. 613. 613. 613. 613. 613. 613. 613. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 614. 619. 621. 621. 621. 621. 621. 621. 622. 622. 629. 629. 629. 629. 629. 630. 638. 638. 638. 638. 645. 645. 645. 650. 651. 651. 652. 652. 652. 652. 652. 652. 652. 652. 652. 652. 652. 655. 655. 655. 655. 657. 657. 658. 658. 658. 658. 658. 659. 659. 659. 659. 661. 812. 812. 812. 812. 812. 812. 812. 812. 812. 812. 812. 812. 812. 814. 814. 815. 815. 815. 815. 818. 818. 818. 818. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 821. 821. 821. 821. 830. 830. 830. 830. 830. 831. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 930. 947. 947. 947. 947. 947. 957. 957. 957. 957. 957. 957. 957. 957. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 958. 960. 960. 960. 960. 960. 960. 960. 960. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 964. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 969. 969. 969. 969. 969. 969. 969. 969. 970. 970. 970. 970. 970. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 971. 976. 976. 976. 977. 977. 977. 978. 978. 978. 978. 978. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 979. 993. 993. 993.1003.1006.1006.1006.1006.1009.1009.1010.1010.1010.1010.1010.1088.1093.1093.1093.1093.1093.1093.1093.1093.1093.1093.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1094.1098.1098.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1102.1104.1107.1107.1107.1107.1107.1107.1108.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1110.1110.1110.1110.1111.1113.1113.1113.1113.1113.1113.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1116.1116.1116.1116.1116.1116.1116.1116.1116.1118.1118.1118.1118.1119.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1127.1127.1128.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1132.1132.1132.1132.1132.1132.1132.1132.1138.1138.1138.1138.1138.1138.1138.1138.1138.1141.1141.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1144.1144.1144.1144.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1147.1147.1147.1147.1147.1147.1152.1152.1152.1152.1166.1166.1304.1304.1308.1308.1308.1308.1310.1310.1310.1310.1310.1310.1310.1310.1325.1338.1338.1338.1338.1338.1338.1340.1340.1340.1340.1341.1341.1341.1341.1342.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1362.1362.1362.1362.1363.1363.1363.1363.1363.1363.1363.1363.1363.1363.1363.1364.1364.1364.1364.1364.1364.1364.1364.1364.1364.1364.1364.1365.1365.1365.1365.1368.1372.1372.1372.1372.1372.1372.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1395.1400.1401.1401.1402.1402.1402.1402.1402.1402.1402.1402.1402.1402.1402.1403.1405.1405.1405.1405.1405.1407.1407.1407.1408.1408.1408.1408.1408.1411.1411.1411.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: 38 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.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 1m50.334s user 0m26.988s sys 0m0.783s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m50.061s user 0m26.667s sys 0m0.796s Creating box around spheres Creating chemgrid maps real 0m35.576s user 0m11.193s sys 0m0.299s Atomic solvent excluded volume calculations underway FORTRAN STOP real 61m26.787s user 20m9.131s sys 0m0.175s 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.