Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-3-02.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 03: No such file or directory. bzcat: Can't open input file 53: 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 03: No such file or directory. bzcat: Can't open input file 53: 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 0m5.012s user 0m0.605s sys 0m1.094s 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 0:1679 spheres. 551. 551. 551. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 710. 712. 712. 712. 712. 712. 712. 714. 714. 714. 714. 714. 719. 721. 722. 722. 722. 722. 722. 730. 730. 730. 730. 732. 732. 732. 732. 733. 733. 733. 733. 733. 734. 734. 734. 734. 734. 734. 734. 734. 734. 734. 734. 734. 734. 734. 735. 735. 735. 735. 735. 735. 735. 735. 736. 740. 740. 741. 741. 741. 741. 741. 741. 741. 741. 741. 745. 745. 745. 745. 745. 745. 745. 745. 745. 745. 745. 745. 745. 745. 745. 745. 745. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 748. 748. 748. 748. 748. 748. 748. 748. 748. 757. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 759.1102.1103.1106.1106.1628.1628.1633.1637.1637.1637.1637.1638.1638.1639.1639.1639.1639.1639.1639.1639.1639.1639.1639.1639.1639.1639.1639.1640.1640.1641.1641.1641.1641.1641.1642.1642.1642.1642.1642.1642.1642.1642.1642.1642.1642.1642.1642.1643.1643.1643.1643.1644.1644.1644.1644.1644.1644.1644.1644.1644.1645.1645.1645.1651.1651.1651.1651.1651.1651.1651.1651.1651.1658.1658.1658.1658.1658.1658.1658.1658.1659.1659.1662.1664.1666.1667.1667.1667.1667.1667.1672.1672.1672.1672.1672.1672.1672.1672.1672.1674.1674.1675.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1703.1703.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1740.1740.1740.1740.1740.1740.1740.1740.1747.1747.1747.1747.1747.1747.1747.1787.1787.1787.1787.1787.1787.1787.1787.1787.1787.1787.1788.1788.1788.1789.1789.1789.1789.1790.1790.1790.1790.1790.1792.1792.1792.1792.1792.1792.1792.1794.1794.1794.1796.1796.1799.1799.1799.1799.1799.1799.1799.1799.1799.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1805.1810.1810.1810.1810.1810.1810.1811.1811.1811.1811.1811.1811.1811.1811.1811.1811.1811.1811.1811.1811.1811.1811.1811.1812.1812.1812.1812.1812.1812.1812.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1815.1819.1819.1819.1819.1820.1820.1820.1820.1820.1820.1820.1820.1820.1820.1820.1820.1825.1826.1838.1838.1838.1838.1839.1839.1839.1839.1839.1841.1841.1841.1841.1841.1841.1841.1847.1847.1881.1881.1881.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1898.1898.1898.1899.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1962.1962.1962.1962.1965.1968.1968.1970.1970.1970.1972.1972.1973.1998.1998.1998.1998.1998.1998.1998.1998.1999.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2002.2002.2002.2002.2003.2003.2003.2004.2004.2004.2004.2004.2004.2004.2004.2004.2004.2005.2005.2005.2005.2028.2028.2028.2028.2033.2033.2033.2033.2033.2034.2043.2043.2043.2043.2071.2071.2071.2071.2075.2075.2075.2075.2075.2075.2075.2075.2075.2075.2075.2075.2075.2075.2075.2098.2098.2099.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2105.2105.2105.2105.2106.2108.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2135.2135.2135.2135.2135.2135.2135.2135.2135.2135.2135.2135.2135.2135.2135.2135.2135.2135.2135.2239.2239.2239.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2240.2241.2241.2241.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2242.2262.2262.2262.2262.2262.2262.2262.2262.2282.2283.2283.2283.2283.2286.2286.2286.2286.2286.2286.2286.2286.2286.2286.2286.2286.2286.2286.2286.2286.2286.2286.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2288.2288.2288.2288.2288.2288.2288.2288.2288.2288.2288.2288.2288.2288.2288.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2290.2290.2290.2290.2290.2290.2290.2295.2298.2298.2298.2298.2317.2317.2317.2317.2317.2317.2317.2317.2317.2321.2321.2321.2321.2321.2321.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2353.2354.2354.2354.2355.2355.2355.2355.2355.2355.2355.2355.2355.2355.2355.2355.2456.2456.2456.2456.2456.2456.2456.2456.2456.2456.2456.2457.2481.2481.2481.2481.2481.2485.2486.2486.2486.2486.2486.2486.2487.2487.2487.2487.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2491.2492.2492.2493.2493.2493.2493.2493.2493.2493.2493.2493.2501.2502.2507.2507.2507.2507.2507.2508.2508.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2510.2510.2510.2510.2513.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2515.2517.2517.2517.2517.2517.2517.2517.2519.2519.2522.2522.2522.2522.2522.2522.2522.2522.2522.2522.2524.2524.2524.2524.2524.2524.2524.2524.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2526.2527.2527.2527.2527.2527.2527.2527.2527.2527.2529.2529.2529.2529.2529.2529.2530.2530.2530.2530.2532.2532.2532.2532.2533.2534.2535.2538.2538.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2551.2552.2552.2552.2552.2552.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2559.2560.2561.2561.2561.2561.2561.2562.2563.2563.2563.2563.2563.2563.2563.2565.2565.2565.2565.2565.2565.2565.2569.2569.2569.2569.2569.2569.2569.2573.2574.2574.2574.2574.2574.2574.2574.2574.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.2595.3515.3515.3515.3515.3515.3515.3515.3515.3515.3515.3519.3519.3519.3519.3525.3525.3525.3525.3525.3527.3527.3527.3527.3527.3527.3527.3527.3529.3529.3529.3529.3558.3558.3558.3558.3558.3558.3558.3558.3558.3558.3558.3558.3559.3562.3562.3563.3563.3563.3563.3563.3563.3563.3563.3563.3567.3567.3567.3567.3567.3567.3567.3567.3567.3567.3567.3567.3567.3567.3568.3568.3568.3568.3568.3568.3568.3568.3568.3568.3568.3568.3568.3568.3568.3568.3568.3568.3568.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3753.3754.3756.3756.3756.3756.3756.3756.3756.3756.3756.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3761.3763.3763.3763.3763.3763.3763.3763.3763.3763.3774.3779.3779.3779.3779.3779.3779.3779.3782.3782.3782.3783.3784.3784.3784.3784.3784.3784.3784.3784.3784.3784.3784.3784.3784.3784.3787.3787.3787.3787.3787.3787.3787.3787.3787.3787.3787.3787.3787.3787.3787.3787.3787.3788.3788.3788.3788.3788.3788.3788.3788.3788.3788.3788.3788.3788.3788.3789.3789.3789.3789.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3790.3791.3791.3791.3791.3791.3791.3791.3791.3791.3791.3791.3791.3791.3791.3791.3791.3791.3791.3791.3809.3809.3809.3809.3809.3809.3809.3809.3809.3809.3811.3813.3813.3813.3813.3813.3816.3816.3816.3816.3818.3818.3818.3818.3818.3818.3818.3818.3818.3818.3818.3818.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3819.3822.3822.3825.3825.3825.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.3826.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4032.4036.4036.4036.4036.4036.4036.4036.4036.4036.4036.4036.4036.4036.4036.4036.4036.4050.4050.4050.4050.4050.4054.4054.4055.4055.4079.4079.4079.4079.4079.4079.4079.4083.4083.4083.4083.4083.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: 35 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.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 0m37.234s user 0m34.835s sys 0m1.345s Adding spheres to tarted electrostatic grid we had to cook * NE2* we had to cook *HNE2* we had to cook *HNE1* Creating DelPhi electrostatic grid real 0m37.590s user 0m34.963s sys 0m1.355s Creating box around spheres Creating chemgrid maps real 1m41.749s user 1m40.865s sys 0m0.483s Atomic solvent excluded volume calculations underway FORTRAN STOP real 21m25.802s user 21m24.457s sys 0m0.206s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ASP 610 has a net charge of -2.0000 End of MakeDOCK sphere and grid generation. Grid preparation completed normally. not ready slept 360 waiting for decoys not ready slept 360 waiting for decoys Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') File "/usr/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1147, in request return self._parse_response(h.getfile(), sock) File "/usr/lib/python2.4/xmlrpclib.py", line 1286, in _parse_response return u.close() File "/usr/lib/python2.4/xmlrpclib.py", line 744, in close raise Fault(**self._stack[0]) xmlrpclib.Fault: slept 360 waiting for decoys Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') File "/usr/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1147, in request return self._parse_response(h.getfile(), sock) File "/usr/lib/python2.4/xmlrpclib.py", line 1286, in _parse_response return u.close() File "/usr/lib/python2.4/xmlrpclib.py", line 744, in close raise Fault(**self._stack[0]) xmlrpclib.Fault: slept 360 waiting for decoys Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') File "/usr/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1147, in request return self._parse_response(h.getfile(), sock) File "/usr/lib/python2.4/xmlrpclib.py", line 1286, in _parse_response return u.close() File "/usr/lib/python2.4/xmlrpclib.py", line 744, in close raise Fault(**self._stack[0]) xmlrpclib.Fault: slept 360 waiting for decoys 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 65 Number of atoms in ligand - 0 IL IS 4144 NR IS- 1 INTERNAL BEGUN INTERNAL COMPLETED 27 NUMLIG IS- 27 TOTAL NUMBER OF ORIENTATIONS WRITEN IS - 0 filtering complete mf7.csh - site preparation complete, preliminary docking queued