Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-23.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 20: No such file or directory. bzcat: Can't open input file 48: 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 20: No such file or directory. bzcat: Can't open input file 48: 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 0m7.016s user 0m0.202s sys 0m0.113s 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 0:1410 spheres. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 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. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 219. 220. 220. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 222. 222. 222. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 228. 228. 228. 229. 229. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 244. 244. 245. 245. 245. 245. 245. 250. 250. 250. 250. 342. 343. 343. 344. 345. 345. 345. 345. 346. 346. 346. 346. 346. 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618. 618. 618. 618. 618. 618. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 631. 638. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 654. 654. 654. 654. 660. 660. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 662. 664. 664. 664. 664. 664. 664. 666. 666. 666. 666. 667. 667. 667. 667. 667. 667. 667. 667. 668. 668. 668. 668. 669. 821. 821. 821. 821. 821. 821. 821. 821. 822. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 830. 839. 839. 839. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 927. 927. 937. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 952. 952. 952. 952. 954. 954. 954. 954. 954. 954. 954. 954. 954. 954. 964. 964. 964. 964. 964. 964. 964. 964. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 967. 967. 967. 967. 967. 967. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 971. 974. 974. 974. 975. 976. 976. 976. 976. 976. 976. 976. 976. 976. 976. 977. 977. 977. 977. 977. 977. 977. 977. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 979. 983. 983. 983. 983. 983. 983. 984. 986. 986. 986. 986. 986. 986. 990. 990. 990. 990. 990. 990.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1010.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1012.1013.1013.1016.1017.1017.1017.1017.1017.1017.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1126.1126.1127.1127.1127.1127.1127.1127.1127.1128.1128.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1134.1134.1135.1135.1135.1135.1135.1135.1135.1135.1137.1137.1138.1138.1138.1138.1138.1139.1139.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1141.1141.1141.1141.1141.1141.1142.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1145.1145.1145.1145.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1147.1147.1147.1147.1147.1147.1147.1147.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1150.1161.1161.1166.1166.1166.1166.1166.1354.1354.1354.1354.1354.1354.1354.1354.1354.1354.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1357.1357.1357.1357.1357.1363.1363.1368.1369.1370.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1373.1375.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1379.1379.1379.1379.1386.1386.1392.1393.1393.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1409.1409.1409.1409.1409.1409.1409.1409.1414.1414.1414.1414.1415.1415.1415.1416.1416.1416.1416.1416.1416.1417.1417.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: 33 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.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 0m50.703s user 0m26.189s sys 0m0.769s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m52.221s user 0m26.045s sys 0m0.757s Creating box around spheres Creating chemgrid maps real 0m17.972s user 0m9.098s sys 0m0.278s Atomic solvent excluded volume calculations underway FORTRAN STOP real 38m45.581s user 17m53.294s sys 0m0.532s 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.