Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-2-33.c.bkslab.org du2 starts 1 molecule processed, 0 errors convert.py (MDL SDF -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. mol2nam v1.9 Structure to Name Conversion OpenEye Scientific Software, February 2009 convert.py (Tripos MOL2 -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. mid: No such file or directory. hi: No such file or directory. lo: No such file or directory. mid: No such file or directory. first try already in then inzinc count is 0 bzcat: Can't open input file 71: No such file or directory. bzcat: Can't open input file 79: 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 71: No such file or directory. bzcat: Can't open input file 79: 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 0m2.970s user 0m0.361s sys 0m0.518s 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 0:1137 spheres. 129. 129. 129. 129. 129. 129. 129. 129. 129. 129. 129. 129. 129. 129. 129. 129. 129. 129. 129. 136. 136. 136. 136. 136. 137. 137. 137. 137. 137. 138. 138. 138. 138. 138. 138. 138. 138. 138. 138. 139. 139. 139. 139. 139. 139. 139. 141. 141. 141. 141. 141. 141. 141. 141. 141. 141. 141. 141. 141. 145. 145. 145. 145. 145. 145. 145. 145. 145. 145. 145. 146. 146. 146. 146. 146. 147. 147. 147. 147. 147. 147. 147. 147. 147. 147. 147. 147. 147. 148. 149. 149. 149. 149. 149. 149. 150. 316. 316. 316. 316. 316. 316. 316. 330. 330. 332. 333. 333. 333. 333. 333. 333. 335. 335. 335. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 342. 342. 342. 342. 342. 342. 344. 344. 344. 344. 345. 345. 347. 347. 347. 349. 349. 349. 349. 349. 349. 349. 349. 349. 349. 349. 349. 349. 349. 349. 349. 349. 354. 354. 354. 359. 359. 359. 359. 359. 359. 359. 359. 359. 359. 359. 359. 359. 359. 360. 360. 360. 360. 360. 360. 360. 361. 362. 362. 363. 363. 363. 364. 364. 364. 364. 364. 364. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 546. 546. 546. 546. 546. 546. 546. 546. 546. 546. 546. 546. 546. 553. 553. 553. 553. 553. 553. 555. 555. 560. 560. 560. 560. 560. 564. 573. 573. 573. 573. 573. 579. 583. 583. 585. 585. 585. 585. 585. 585. 585. 585. 602. 602. 602. 602. 602. 602. 602. 602. 602. 603. 603. 603. 603. 603. 603. 603. 603. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 605. 608. 820. 820. 823. 829. 829. 829. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 834. 834. 834. 834. 834. 834. 834. 834. 834. 834. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 835. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 837. 837. 837. 837. 837. 837. 837. 837. 841. 841. 841. 841. 850. 850. 850. 850. 851. 851. 852. 852. 852. 852. 852. 852. 859. 859. 859. 859. 859. 859. 859. 859. 859. 859. 866. 866. 866. 911. 911. 911. 911. 913. 913. 913. 913. 913. 913. 913. 913. 913. 915. 920. 920. 920. 920. 920. 923. 923. 923. 923. 923. 923. 924. 924. 924. 924. 924. 924. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 925. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 982. 982. 982. 982.1200.1200.1200.1200.1249.1249.1249.1249.1249.1249.1249.1249.1249.1249.1249.1249.1249.1252.1252.1252.1394.1394.1394.1394.1394.1394.1403.1403.1403.1403.1403.1403.1403.1661.1661.1661.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1668.1669.1669.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1674.1675.1675.1675.1675.1675.1675.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1677.1677.1677.1677.1677.1677.1677.1677.1678.1678.1679.1679.1679.1679.1680.1680.1680.1680.1680.1680.1680.1680.1680.1680.1681.1681.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1683.1683.1683.1683.1683.1683.1683.1683.1683.1947.1947.1947.1947.1947.1947.2189.2192.2192.2192.2192.2192.2192.2192.2192.2192.2192.2192.2192.2192.2192.2192.2192.2192.2192.2193.2195.2198.2198.2198.2198.2199.2199.2199.2199.2199.2199.2199.2199.2199.2199.2199.2201.2201.2201.2201.2201.2201.2202.2203.2208.2208.2209.2211.2211.2212.2212.2212.2213.2213.2215.2215.2215.2215.2215.2215.2215.2216.2216.2216.2216.2216.2216.2216.2216.2216.2216.2216.2216.2217.2217.2217.2217.2217.2217.2217.2218.2218.2218.2218.2218.2218.2218.2218.2218.2219.2222.2222.2222.2222.2222.2222.2222.2222.2222.2222.2222.2222.2222.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2224.2225.2225.2225.2225.2225.2225.2229.2230.2230.2230.2230.2230.2230.2230.2230.2230.2230.2230.2230.2230.2230.2230.2230.2231.2231.2231.2232.2232.2232.2232.2232.2233.2233.2233.2233.2233.2233.2233.2233.2233.2233.2233.2233.2233.2233.2233.2233.2233.2233.2233.2233.2234.2235.2235.2235.2236.2237.2237.2237.2237.2237.2238.2238.2238.2238.2238.2238.2238.2238.2238.2238.2238.2238.2238.2238.2238.2239.2239.2239.2239.2239.2244.2244.2244.2244.2244.2244.2244.2244.2244.2244.2244.2244.2245.2245.2245.2245.2245.2245.2245.2245.2245.2251.2251.2251.2251.2251.2251.2251.2251.2252.2254.2254.2255.2255.2255.2255.2255.2255.2256.2256.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2258.2258.2258.2258.2258.2258.2258.2258.2258.2258.2258.2260.2260.2260.2269.2269.2269.2270.2272.2272.2272.2272.2272.2272.2272.2273.2273.2273.2273.2273.2273.2273.2273.2275.2276.2276.2276.2276.2276.2276.2277.2277.2277.2283.2284.2284.2284.2284.2284.2284.2284.2284.2284.2284.2284.2284.2284.2284.2284.2284.2284.2284.2285.2285.2285.2285.2285.2285.2285.2285.2285.2289.2289.2289.2289.2289.2289.2292.2292.2294.2294.2294.2294.2297.2300.2300.2301.2301.2301.2301.2301.2306.2306.2306.2306.2306.2306.2306.2307.2308.2308.2308.2308.2308.2308.2309.2311.2311.2313.2313.2313.2313.2313.2313.2313.2320.2320.2320.2320.2320.2322.2323.2323.2323.2323.2324.2325.2325.2325.2325.2364.2364.2364.2364.2364.2364.2364.2364.2364.2364.2364.2364.2364.2364.2395.2397.2397.2397.2397.2397.2397.2403.2403.2403.2403.2403.2403.2403.2403.2403.2403.2403.2403.2403.2403.2403.2403.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 0m36.196s user 0m33.801s sys 0m1.364s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m36.230s user 0m33.895s sys 0m1.376s Creating box around spheres Creating chemgrid maps real 1m17.789s user 1m17.040s sys 0m0.476s Atomic solvent excluded volume calculations underway FORTRAN STOP real 25m45.542s user 25m44.848s sys 0m0.239s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: NAP 500 has a net charge of -2.0000 !!! WARNING: NAP 500 has a net charge of -2.0000 !!! WARNING: NAP 500 has a net charge of -2.0000 End of MakeDOCK sphere and grid generation. Grid preparation completed normally. PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. File name = ../grids/distmap In source file scoreopt_so.f, at line number 625 PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. File name = ../grids/distmap In source file scoreopt_so.f, at line number 625 PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. File name = ../grids/distmap In source file scoreopt_so.f, at line number 625 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 32 Number of atoms in ligand - 0 IL IS 2403 NR IS- 1 INTERNAL BEGUN INTERNAL COMPLETED 21 NUMLIG IS- 21 TOTAL NUMBER OF ORIENTATIONS WRITEN IS - 1 filtering complete mf7.csh - site preparation complete, preliminary docking queued