Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-10.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 39: No such file or directory. bzcat: Can't open input file 81: 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 39: No such file or directory. bzcat: Can't open input file 81: 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 0m2.408s user 0m0.402s sys 0m0.307s 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 0:1538 spheres. 126. 127. 127. 127. 127. 127. 127. 131. 131. 131. 131. 131. 131. 131. 131. 134. 221. 221. 221. 221. 221. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 225. 226. 226. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 228. 228. 228. 228. 228. 233. 233. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 237. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 238. 240. 241. 242. 242. 242. 242. 242. 243. 243. 243. 243. 243. 243. 244. 245. 245. 245. 246. 246. 246. 246. 246. 246. 246. 248. 248. 248. 248. 248. 248. 248. 248. 248. 252. 253. 254. 254. 254. 255. 255. 255. 255. 255. 255. 255. 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689. 689. 689. 689. 817. 817. 817. 817. 817. 817. 817. 817. 821. 822. 822. 822. 838. 838. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 844. 844. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 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. 849. 849. 849. 849. 849. 853. 853. 853. 853. 853. 853. 853. 853. 853. 853. 853. 853. 853. 853. 853. 853. 856. 856. 856. 856. 856. 856. 856. 857. 857. 857. 857. 857. 857. 857. 857. 857. 857. 858. 858. 861. 861. 862. 863. 864. 864. 865. 865. 866. 866. 866. 867. 867. 867. 867. 867. 867. 867. 867. 867. 867. 867. 867. 867. 867. 868. 868. 868. 868. 868. 868. 868. 868. 868. 869. 869. 869. 869. 869. 869. 869. 869. 869. 869. 869. 869. 869. 869. 869. 869. 869. 871. 871. 871. 871. 871. 871. 871. 871. 871. 872. 872. 874. 874. 874. 874. 874. 874. 874. 879. 879. 879. 879. 879. 879. 879. 879. 880. 880. 880. 880. 880. 880. 880. 880. 882. 882. 882. 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914.1200.1200.1200.1200.1200.1200.1200.1200.1200.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1214.1214.1214.1214.1216.1216.1216.1216.1216.1216.1216.1217.1217.1217.1217.1217.1217.1217.1217.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1224.1224.1224.1224.1225.1225.1225.1229.1230.1230.1230.1230.1230.1230.1230.1230.1230.1230.1230.1230.1230.1230.1231.1231.1231.1231.1231.1231.1231.1238.1238.1238.1238.1238.1238.1238.1238.1238.1238.1238.1238.1252.1252.1252.1258.1258.1258.1258.1258.1258.1258.1258.1258.1258.1258.1258.1258.1261.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1262.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1263.1264.1264.1264.1264.1264.1264.1264.1264.1264.1264.1264.1264.1264.1264.1267.1267.1267.1267.1267.1267.1295.1295.1295.1295.1295.1295.1295.1295.1295.1295.1295.1297.1297.1297.1297.1297.1297.1297.1297.1297.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1302.1302.1303.1303.1303.1303.1303.1303.1303.1303.1303.1313.1313.1314.1315.1315.1315.1315.1315.1315.1315.1315.1315.1315.1315.1315.1315.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1316.1329.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1331.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1332.1333.1333.1333.1333.1334.1334.1334.1334.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1339.1339.1339.1339.1339.1339.1339.1339.1339.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1340.1359.1359.1359.1359.1360.1360.1361.1361.1361.1361.1362.1362.1363.1363.1363.1363.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: 37 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.FORTRAN STOP Adding essential hydrogens to receptor 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 0m27.930s user 0m21.906s sys 0m0.624s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m26.702s user 0m22.998s sys 0m0.661s Creating box around spheres Creating chemgrid maps real 0m19.381s user 0m18.547s sys 0m0.255s Atomic solvent excluded volume calculations underway FORTRAN STOP real 28m16.510s user 28m15.138s sys 0m0.084s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar failed to get similars