Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-33.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 59: No such file or directory. bzcat: Can't open input file 66: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. count is 0 bzcat: Can't open input file 59: No such file or directory. bzcat: Can't open input file 69: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. bzcat: Can't open input file 59: No such file or directory. bzcat: Can't open input file 66: No such file or directory. bzcat: Can't open input file 59: No such file or directory. bzcat: Can't open input file 69: No such file or directory. 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 0m2.210s user 0m0.210s sys 0m0.379s 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 0:1288 spheres. 189. 189. 189. 189. 189. 189. 189. 189. 189. 190. 191. 191. 191. 191. 191. 191. 191. 191. 191. 191. 191. 191. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 197. 197. 197. 197. 197. 198. 198. 198. 198. 198. 198. 198. 199. 199. 199. 202. 202. 202. 202. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 204. 205. 205. 205. 205. 205. 205. 205. 205. 205. 205. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 207. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 211. 211. 211. 211. 212. 214. 215. 215. 215. 215. 215. 215. 216. 216. 216. 216. 216. 216. 216. 216. 216. 216. 216. 216. 216. 216. 216. 216. 217. 217. 217. 217. 218. 218. 219. 219. 219. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 221. 221. 221. 222. 222. 222. 223. 223. 223. 226. 226. 226. 226. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 227. 230. 231. 231. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 234. 234. 234. 234. 234. 234. 234. 234. 234. 235. 235. 235. 235. 235. 238. 238. 238. 239. 239. 240. 240. 247. 248. 248. 248. 248. 248. 248. 248. 248. 254. 254. 254. 254. 254. 254. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 264. 264. 266. 266. 266. 266. 266. 266. 266. 266. 266. 266. 266. 266. 266. 334. 334. 334. 334. 334. 334. 334. 334. 334. 334. 334. 335. 335. 335. 335. 335. 336. 336. 336. 336. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 338. 338. 338. 338. 338. 338. 338. 338. 338. 344. 344. 344. 350. 350. 350. 350. 350. 350. 350. 350. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 367. 367. 367. 367. 367. 367. 367. 367. 367. 379. 379. 379. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 384. 384. 384. 384. 384. 384. 384. 384. 478. 481. 481. 482. 482. 482. 482. 482. 482. 482. 482. 483. 483. 483. 483. 483. 483. 483. 484. 484. 484. 484. 484. 484. 484. 484. 484. 484. 484. 485. 485. 485. 485. 485. 485. 485. 485. 485. 485. 485. 485. 485. 485. 485. 485. 485. 485. 485. 486. 486. 486. 486. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 487. 517. 517. 517. 517. 517. 517. 517. 520. 520. 520. 520. 520. 520. 520. 522. 524. 524. 549. 549. 549. 549. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 555. 555. 555. 555. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 628. 628. 628. 630. 630. 630. 630. 630. 630. 633. 633. 633. 633. 633. 633. 633. 635. 638. 638. 638. 638. 638. 802. 802. 808. 810. 810. 810. 811. 811. 811. 811. 811. 811. 811. 811. 811. 811. 811. 811. 811. 811. 811. 811. 813. 813. 813. 813. 813. 813. 813. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 816. 819. 819. 819. 819. 819. 819. 819. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 824. 825. 826. 826. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 829. 831. 831. 832. 832. 833. 833. 833. 833. 838. 838. 839. 839. 839. 839. 839. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 840. 841. 841. 842. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 843. 846. 846. 846. 846. 846. 847. 847. 847. 847. 849. 849. 849. 849. 849. 849. 849. 854. 854. 854. 854. 854. 854. 854. 854. 854. 854. 854. 854. 854. 855. 855. 855. 855. 855. 855. 855. 855. 856. 856. 856. 856. 870. 870. 870. 871. 871. 871. 871. 871. 871. 871. 871. 871. 871. 871. 871. 871. 871. 871. 871. 871. 871. 871. 874. 874. 874. 878. 878. 879. 879. 879. 879. 879. 879. 879. 879. 879. 879. 879. 879. 879. 880. 880. 880. 880. 880. 880. 880. 880. 880.1176.1176.1177.1177.1177.1177.1177.1177.1177.1177.1177.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1185.1185.1185.1185.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1190.1191.1191.1191.1191.1191.1191.1191.1197.1197.1197.1197.1197.1197.1197.1197.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1198.1199.1199.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1221.1221.1221.1221.1221.1221.1221.1224.1225.1227.1227.1227.1227.1227.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1229.1229.1229.1230.1230.1230.1230.1230.1230.1230.1230.1230.1230.1230.1230.1230.1230.1232.1232.1232.1232.1232.1234.1234.1234.1234.1234.1234.1234.1235.1235.1235.1235.1235.1235.1273.1273.1273.1273.1273.1273.1273.1273.1273.1273.1273.1273.1274.1282.1282.1282.1282.1282.1282.1282.1282.1282.1285.1286.1286.1287.1287.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1289.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1295.1295.1295.1295.1295.1295.1295.1295.1295.1295.1295.1295.1295.1295.1295.1295.1402.1403.1403.1403.1403.1403.1403.1405.1405.1405.1405.1405.1405.1405.1405.1405.1405.1405.1405.1405.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.1406.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: 23 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23.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 0m25.855s user 0m23.455s sys 0m0.574s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m25.318s user 0m23.567s sys 0m0.574s Creating box around spheres Creating chemgrid maps real 0m12.797s user 0m11.999s sys 0m0.230s Atomic solvent excluded volume calculations underway FORTRAN STOP real 20m29.517s user 20m29.087s sys 0m0.037s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. going into second inactives test after second inactives finished ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory Permission denied, please try again. ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory Permission denied, please try again. ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory Permission denied (publickey,gssapi-with-mic,password). FILTER PROGRAM THIS PROGRAM FILTERS ATOMIC COORDINATE FILES BASED ON DISTANCE AND SEQUENCE CRITERIA name of file to filter by - xtal-lig.pdb filter by atom names or numbers in receptor(na/nu)? residue/ligand orientation number increment filter? -100000 Filter for MS run?(Y/N) N Either names or numbers of the atoms to filter by, as they appear in the pdb, with boolean and/or operators if such apply between them. Maximum of one boolean per two filter atoms. name of ligand file- rec.pdb names of ligand atoms to match against receptor filters. Include boolean and/ors between EACH atom specified. LIGAND ATOM 1ISALL internal filtering? Y distance cutoffs for each of the receptor atoms specified- 25.00000 output filename- poc.txt number of allowed ligand contacts in an all-filter? LIGBUM IS- 0 IR IS 44 Number of atoms in ligand - 0 IL IS 2255 NR IS- 1 INTERNAL BEGUN INTERNAL COMPLETED 25 NUMLIG IS- 25 TOTAL NUMBER OF ORIENTATIONS WRITEN IS - 0 filtering complete mf7.csh - site preparation complete, preliminary docking queued