Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-4-20.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 23: No such file or directory. bzcat: Can't open input file 60: 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 25: No such file or directory. bzcat: Can't open input file 84: 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 23: No such file or directory. bzcat: Can't open input file 60: No such file or directory. bzcat: Can't open input file 25: No such file or directory. bzcat: Can't open input file 84: 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 0m5.709s user 0m0.801s sys 0m0.835s 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 0:1238 spheres. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 551. 555. 555. 555. 555. 555. 555. 555. 555. 555. 555. 709. 709. 709. 709. 709. 714. 714. 714. 714. 714. 714. 716. 718. 718. 718. 718. 718. 718. 720. 722. 722. 722. 722. 722. 722. 730. 730. 730. 730. 730. 730. 732. 733. 733. 733. 733. 733. 733. 733. 733. 733. 734. 734. 734. 734. 734. 734. 734. 734. 734. 734. 734. 735. 735. 735. 735. 735. 735. 735. 735. 735. 735. 740. 740. 741. 741. 741. 741. 741. 741. 741. 741. 745. 745. 745. 745. 745. 745. 745. 745. 745. 745. 747. 747. 747. 747. 748. 748. 748. 748. 748. 749. 749. 749. 749. 749. 749. 749. 749. 749. 757. 757. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758. 758.1099.1102.1103.1103.1103.1106.1106.1106.1106.1106.1106.1106.1628.1630.1633.1633.1633.1636.1637.1637.1637.1637.1638.1638.1638.1638.1638.1638.1638.1638.1638.1638.1638.1638.1638.1638.1638.1639.1640.1640.1640.1640.1640.1640.1640.1640.1641.1641.1641.1641.1641.1641.1641.1642.1642.1642.1642.1642.1642.1642.1642.1642.1642.1642.1643.1643.1643.1643.1643.1644.1644.1644.1645.1645.1645.1651.1651.1651.1651.1651.1651.1651.1651.1651.1651.1651.1651.1651.1657.1657.1657.1657.1657.1658.1658.1658.1658.1658.1658.1658.1659.1663.1667.1667.1667.1667.1667.1672.1672.1672.1672.1672.1672.1674.1674.1675.1675.1675.1675.1675.1675.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1703.1728.1728.1728.1728.1728.1728.1728.1728.1728.1728.1740.1747.1747.1747.1747.1747.1747.1747.1747.1747.1747.1751.1792.1792.1792.1792.1792.1794.1794.1796.1796.1798.1798.1799.1799.1799.1799.1799.1799.1799.1799.1799.1799.1799.1799.1799.1801.1801.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1805.1810.1810.1810.1810.1810.1810.1810.1810.1811.1811.1811.1811.1811.1811.1811.1811.1811.1811.1812.1812.1812.1812.1812.1812.1812.1812.1812.1812.1812.1812.1812.1812.1812.1812.1812.1812.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1813.1819.1819.1819.1820.1820.1820.1820.1820.1820.1820.1820.1820.1820.1820.1820.1820.1820.1820.1820.1826.1826.1827.1838.1838.1838.1838.1839.1839.1839.1839.1839.1839.1839.1841.1841.1841.1841.1841.1841.1841.1841.1843.1843.1847.1847.1847.1847.1850.1852.1852.1862.1862.1862.1862.1862.1866.1866.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1882.1898.1898.1898.1899.1899.1901.1901.1901.1901.1901.1901.1901.1901.1901.1901.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1915.1962.1965.1965.1965.1965.1965.1965.1965.1965.1965.1966.1966.1966.1966.1972.1973.1973.1998.1998.1998.1998.1998.1999.1999.1999.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2001.2002.2002.2002.2002.2002.2003.2004.2004.2004.2004.2004.2005.2005.2005.2028.2028.2028.2033.2033.2033.2033.2043.2043.2043.2043.2043.2043.2043.2043.2043.2071.2071.2071.2075.2075.2075.2075.2088.2088.2090.2090.2090.2090.2090.2090.2090.2090.2090.2090.2090.2090.2091.2091.2098.2098.2099.2100.2100.2100.2105.2105.2105.2106.2106.2106.2108.2108.2108.2108.2108.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2111.2135.2285.2285.2285.2285.2285.2286.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2287.2288.2288.2288.2288.2288.2288.2288.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2289.2290.2290.2290.2290.2454.2454.2454.2454.2454.2454.2456.2456.2456.2456.2456.2456.2456.2456.2456.2457.2481.2481.2481.2481.2481.2486.2486.2486.2487.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2491.2491.2492.2493.2493.2493.2493.2493.2499.2503.2507.2507.2508.2509.2509.2509.2510.2510.2510.2513.2513.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2515.2515.2515.2515.2515.2515.2515.2517.2517.2517.2517.2517.2517.2517.2519.2519.2522.2522.2522.2522.2522.2522.2522.2523.2523.2523.2524.2524.2524.2524.2524.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2526.2526.2527.2527.2527.2527.2527.2527.2529.2529.2529.2529.2530.2530.2530.2532.2532.2532.2538.2538.2538.2538.2538.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2539.2551.2551.2551.2551.2551.2551.2551.2551.2551.2552.2552.2552.2552.2552.2552.2552.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2559.2559.2559.2559.2559.2560.2560.2561.2561.2561.2561.2561.2561.2561.2561.2562.2562.2563.2563.2563.2563.2563.2563.2563.2563.2563.2563.2563.2563.2563.2564.2565.2565.2565.2565.2565.2565.2565.2569.2569.2569.2569.2569.2569.2569.2569.2574.2574.2574.2574.2574.2574.2574.2574.2595.2595.2595.3490.3490.3490.3490.3490.3490.3490.3491.3491.3491.3492.3492.3492.3492.3492.3494.3494.3494.3494.3494.3494.3708.3711.3712.3713.3713.3713.3713.3713.3713.3713.3713.3713.3713.3716.3716.3716.3716.3717.3718.3718.3718.3718.3718.3718.3718.3718.3718.3718.3718.3718.3718.3718.3718.3718.3720.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3721.3722.3722.3722.3722.3722.3722.3722.3722.3722.3722.3722.3722.3722.3722.3723.3723.3723.3723.3723.3723.3723.3723.3723.3723.3723.3723.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3724.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3725.3924.3924.3924.3924.3924.3924.3924.3928.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3929.3938.3938.3938.3938.3938.3938.3941.3941.3942.3942.3942.3942.3943.3943.3943.3943.3943.3943.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: 22 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22.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 0m40.465s user 0m36.970s sys 0m1.506s 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 0m41.049s user 0m36.937s sys 0m1.551s Creating box around spheres Creating chemgrid maps real 2m0.908s user 1m59.595s sys 0m0.532s Atomic solvent excluded volume calculations underway FORTRAN STOP real 26m7.751s user 26m3.507s sys 0m0.310s 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 not ready slept 360 waiting for decoys not ready slept 360 waiting for decoys not ready slept 360 waiting for decoys not ready slept 360 waiting for decoys not ready slept 360 waiting for decoys not ready slept 360 waiting for decoys not ready slept 360 waiting for decoys not ready slept 360 waiting for decoys not ready slept 360 waiting for decoys not ready slept 360 waiting for decoys not ready slept 360 waiting for decoys 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 46 Number of atoms in ligand - 0 IL IS 4032 NR IS- 1 INTERNAL BEGUN INTERNAL COMPLETED 23 NUMLIG IS- 23 TOTAL NUMBER OF ORIENTATIONS WRITEN IS - 0 filtering complete mf7.csh - site preparation complete, preliminary docking queued Unmatched ".