Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-07.c.bkslab.org du2 starts 1 molecule processed, 0 errors first try already in then inzinc count is 0 nothing to compress count is 0 nothing to compress nothing to compress 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 0m46.661s user 0m0.355s sys 0m0.138s 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 0:1264 spheres. 79. 79. 82. 82. 82. 82. 82. 82. 82. 84. 85. 85. 85. 87. 87. 87. 87. 87. 89. 89. 89. 89. 90. 90. 90. 90. 90. 90. 90. 90. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 94. 94. 94. 94. 94. 94. 94. 94. 94. 94. 94. 94. 94. 103. 103. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 223. 223. 223. 223. 223. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 242. 242. 255. 255. 256. 256. 256. 256. 256. 256. 259. 259. 259. 259. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 267. 268. 268. 268. 269. 269. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 272. 272. 272. 272. 272. 272. 277. 277. 277. 277. 278. 278. 278. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 281. 281. 281. 297. 297. 297. 297. 297. 297. 297. 303. 303. 305. 306. 306. 312. 312. 312. 315. 316. 316. 316. 316. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 423. 423. 423. 429. 429. 429. 429. 429. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 431. 431. 431. 435. 435. 435. 435. 438. 439. 439. 439. 439. 439. 439. 439. 439. 439. 445. 445. 445. 445. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 448. 448. 448. 448. 448. 448. 448. 448. 448. 448. 448. 448. 451. 451. 451. 451. 452. 452. 452. 452. 452. 452. 452. 452. 452. 452. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 454. 454. 454. 454. 454. 454. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 457. 457. 458. 458. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 468. 471. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 473. 473. 473. 475. 475. 475. 475. 482. 482. 482. 486. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 488. 488. 488. 488. 488. 488. 488. 488. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 497. 546. 548. 549. 549. 692. 692. 692. 692. 692. 692. 692. 692. 693. 694. 694. 694. 694. 695. 695. 695. 696. 711. 711. 728. 728. 728. 728. 728. 728. 730. 730. 730. 730. 730. 731. 731. 731. 731. 731. 731. 733. 733. 733. 733. 744. 744. 746. 746. 747. 747. 747. 747. 747. 747. 747. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 749. 749. 749. 751. 754. 754. 755. 755. 755. 755. 755. 755. 755. 755. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 764. 764. 766. 767. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 776. 785. 794. 794. 794. 794. 794. 794. 794. 800. 800. 800. 800. 801. 801. 801. 806. 806. 806. 806. 806. 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999.1001.1002.1002.1002.1002.1002.1002.1002.1002.1002.1002.1002.1002.1004.1004.1005.1005.1006.1007.1007.1007.1009.1009.1009.1009.1009.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1014.1014.1014.1014.1014.1017.1023.1023.1023.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1026.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1141.1152.1152.1152.1152.1152.1152.1152.1152.1152.1160.1160.1160.1160.1176.1176.1176.1176.1179.1179.1179.1179.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1187.1188.1188.1188.1188.1188.1188.1189.1191.1191.1191.1191.1191.1191.1191.1191.1192.1192.1192.1192.1197.1197.1197.1197.1197.1197.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1199.1199.1199.1199.1199.1199.1199.1199.1199.1200.1200.1201.1201.1201.1209.1217.1217.1217.1217.1217.1217.1217.1217.1232.1232.1232.1235.1235.1235.1235.1235.1236.1236.1236.1343.1346.1346.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1351.1351.1351.1355.1355.1355.1355.1359.1365.1365.1365.1368.1368.1368.1368.1368.1368.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1374.1374.1374.1374.1374.1374.1374.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1388.1388.1388.1391.1392.1392.1392.1392.1392.1392.1392.1393.1395.1395.1395.1395.1395.1395.1395.1396.1396.1402.1405.1405.1406.1407.1407.1407.1407.1407.1407.1407.1407.1407.1407.1408.1408.1408.1408.1408.1408.1410.1412.1412.1417.1417.1417.1417.1417.1461.1461.1461.1461.1461.1461.1461.1468.1610.1611.1612.1612.1612.1614.1614.1614.1614.1614.1614.1614.1614.1614.1614.1614.1614.1614.1614.1614.1614.1615.1615.1615.1616.1616.1630.1630.1630.1632.1632.1650.1650.1650.1650.1651.1651.1651.1651.1651.1651.1652.1652.1657.1657.1657.1657.1664.1664.1664.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1669.1669.1669.1671.1674.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1676.1676.1676.1676.1681.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1686.1686.1686.1686.1686.1686.1686.1686.1686.1696.1696.1696.1696.1696.1696.1696.1696.1714.1714.1714.1714.1720.1720.1721.1721.1721.1722.1722.1726.1726.1726.1726.1726.1726.1727.1728.1728.1728.1728.1728.1728.1728.1728.1730.1730.1730.1730.1730.1730.1733.1733.1734.1736.1736.1739.1739.1739.1739.1739.1747.1747.1747.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: 62 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. 55. 56. 57. 58. 59. 60. 61. 62.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 1m2.099s user 0m24.557s sys 0m0.631s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m21.249s user 0m23.225s sys 0m0.596s Creating box around spheres Creating chemgrid maps real 0m54.836s user 0m16.002s sys 0m0.190s Atomic solvent excluded volume calculations underway FORTRAN STOP real 89m50.407s user 30m42.727s sys 0m0.219s 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.