Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-06.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 32: No such file or directory. bzcat: Can't open input file 71: 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 32: No such file or directory. bzcat: Can't open input file 71: 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 0m41.201s user 0m0.298s sys 0m0.126s 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 0:1284 spheres. 82. 82. 82. 82. 85. 87. 89. 89. 89. 89. 89. 89. 89. 90. 90. 90. 90. 90. 90. 90. 90. 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. 95. 95. 95. 95. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 242. 242. 242. 242. 242. 242. 242. 255. 255. 255. 255. 256. 256. 256. 256. 256. 256. 256. 256. 256. 256. 259. 259. 259. 259. 259. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 267. 267. 267. 268. 268. 268. 268. 268. 268. 271. 271. 271. 271. 271. 271. 271. 271. 272. 272. 272. 272. 272. 272. 272. 272. 277. 277. 277. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 280. 280. 280. 280. 280. 280. 280. 281. 296. 296. 296. 296. 296. 296. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 312. 313. 313. 313. 313. 313. 313. 313. 313. 313. 316. 420. 420. 420. 420. 426. 426. 426. 429. 429. 429. 429. 429. 429. 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489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 490. 493. 497. 690. 691. 692. 692. 692. 692. 692. 692. 692. 693. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 696. 711. 730. 730. 730. 730. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 732. 732. 733. 733. 744. 745. 745. 746. 746. 746. 746. 746. 746. 746. 746. 746. 746. 746. 747. 747. 747. 747. 747. 747. 747. 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. 748. 748. 748. 748. 748. 749. 749. 751. 754. 754. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 756. 765. 765. 766. 766. 767. 767. 767. 767. 767. 774. 775. 775. 775. 775. 793. 793. 793. 799. 799. 799. 800. 800. 800. 801. 801. 805. 805. 805. 805. 805. 807. 807. 809. 809. 809. 809. 809. 809. 811. 812. 812. 812. 812. 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999.1000.1001.1002.1002.1002.1002.1002.1004.1004.1006.1007.1007.1007.1007.1007.1007.1007.1009.1010.1010.1010.1010.1010.1010.1010.1010.1010.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1014.1023.1023.1023.1025.1025.1025.1025.1025.1025.1025.1026.1026.1026.1026.1026.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1027.1144.1144.1150.1150.1150.1150.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1153.1160.1160.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1170.1175.1176.1176.1179.1179.1179.1179.1179.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1182.1187.1188.1188.1188.1189.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1192.1192.1192.1192.1192.1197.1197.1198.1198.1198.1198.1198.1198.1198.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1200.1200.1200.1200.1200.1200.1200.1200.1200.1200.1200.1200.1200.1200.1200.1200.1200.1201.1209.1209.1209.1209.1209.1217.1217.1217.1223.1223.1223.1223.1223.1223.1223.1223.1223.1223.1223.1223.1223.1223.1223.1223.1340.1340.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1346.1346.1346.1349.1349.1349.1349.1349.1351.1351.1351.1351.1356.1356.1357.1357.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1359.1359.1359.1359.1363.1365.1365.1365.1367.1367.1367.1367.1368.1368.1368.1368.1368.1368.1368.1368.1368.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1374.1374.1374.1374.1374.1374.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1377.1384.1385.1385.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1391.1391.1392.1392.1392.1392.1392.1392.1393.1393.1393.1395.1395.1395.1395.1395.1395.1395.1395.1395.1402.1402.1403.1403.1405.1405.1406.1406.1406.1406.1406.1406.1407.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1409.1409.1409.1410.1410.1412.1413.1413.1413.1417.1417.1434.1434.1436.1436.1630.1630.1630.1630.1630.1630.1630.1630.1630.1630.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1648.1648.1648.1648.1650.1650.1650.1651.1651.1651.1651.1652.1653.1653.1653.1666.1666.1666.1666.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1669.1669.1669.1669.1674.1674.1674.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1686.1686.1686.1687.1687.1694.1694.1694.1694.1695.1713.1713.1713.1713.1719.1719.1719.1720.1720.1720.1725.1725.1725.1725.1725.1725.1725.1725.1725.1727.1729.1729.1729.1729.1729.1729.1732.1732.1732.1732.1732.1732.1732.1732.1733.1733.1733.1733.1735.1738.1738.1755.1755.1755.1755.1755.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: 40 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.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 1m24.468s user 0m22.247s sys 0m0.564s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m19.379s user 0m21.181s sys 0m0.597s Creating box around spheres Creating chemgrid maps real 0m51.892s user 0m14.051s sys 0m0.224s Atomic solvent excluded volume calculations underway FORTRAN STOP real 76m54.554s user 26m32.857s sys 0m0.115s 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.