Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-09.c.bkslab.org du2 starts 1 molecule processed, 0 errors convert.py (MDL SDF -> Isomeric SMILES): mols in: 2 mols out: 2 Total: 2 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. first try already in then inzinc count is 0 bzcat: Can't open input file 84: No such file or directory. bzcat: Can't open input file 03: No such file or directory. bzcat: Can't open input file 34: No such file or directory. bzcat: Can't open input file 33: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 2 mols out: 2 Total: 2 mols processed. count is 0 bzcat: Can't open input file 13: No such file or directory. bzcat: Can't open input file 63: 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 84: No such file or directory. bzcat: Can't open input file 03: No such file or directory. bzcat: Can't open input file 34: No such file or directory. bzcat: Can't open input file 33: No such file or directory. bzcat: Can't open input file 13: No such file or directory. bzcat: Can't open input file 63: 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 0m3.295s user 0m0.532s sys 0m0.303s 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 0:1217 spheres. 370. 405. 406. 407. 407. 407. 407. 407. 409. 409. 409. 409. 409. 409. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 421. 422. 422. 422. 422. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 450. 451. 451. 451. 452. 452. 452. 452. 453. 453. 453. 453. 453. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 456. 456. 456. 456. 456. 456. 456. 456. 488. 488. 488. 488. 488. 488. 488. 657. 735. 735. 741. 744. 744. 744. 744. 744. 744. 744. 744. 745. 745. 745. 745. 745. 745. 745. 746. 746. 754. 754. 754. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 755. 756. 896. 896. 896. 896. 896. 896. 896. 896. 896. 896. 896. 896. 896. 899. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 900. 901. 901. 901. 901. 905. 905. 905. 905. 905. 905. 905. 905. 905. 907. 908. 908. 908. 908. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 910. 913. 914. 914. 914. 914. 920. 922. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 926. 927. 927. 927. 927. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 931. 933. 933. 935. 936. 936. 936. 936. 936. 936. 936. 936. 936. 937. 937. 938.1042.1044.1044.1044.1044.1044.1044.1044.1044.1044.1044.1044.1044.1044.1044.1045.1045.1045.1045.1045.1045.1047.1048.1051.1051.1052.1052.1052.1052.1052.1052.1052.1052.1052.1052.1052.1583.1583.1583.1583.1583.1583.1583.1590.1599.1599.1599.1599.1599.1599.1599.1599.1599.1605.1607.1607.1607.1607.1607.1607.1607.1607.1607.1607.1607.1607.1608.1608.1608.1608.1608.1608.1608.1608.1608.1608.1608.1608.1610.1614.1618.1618.1618.1620.1620.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1621.1623.1623.1624.1624.1624.1624.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1625.1629.1629.1629.1629.1629.1629.1629.1629.1629.1629.1629.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1631.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1632.1633.1633.1634.1634.1634.1634.1635.1635.1635.1635.1635.1635.1635.1635.1635.1635.1635.1635.1635.1635.1635.1635.1635.1635.1640.1640.1640.1640.1640.1640.1641.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1643.1735.1743.1743.1745.1745.1745.1745.1745.1745.1745.1746.1749.1754.1754.1755.1755.1761.1766.1767.1769.1769.1769.1769.1769.1769.1769.1769.1769.1769.1769.1770.1770.1770.1771.1771.1771.1771.1781.1781.1781.1781.1781.1781.1783.1783.1783.1791.1791.1791.1791.1791.1791.1791.1791.1791.1791.1791.1791.1791.1793.1793.1793.1794.1794.1794.1794.1794.1794.1794.1794.1794.1794.1794.1794.1794.1794.1802.1802.1802.1804.1804.1804.1807.1807.1807.1807.1807.1807.1807.1807.1808.1808.1808.1808.1808.1808.1809.1809.1810.1810.1810.1810.1810.1810.1810.1810.1810.1811.1811.1811.1811.1811.1835.1835.1835.1835.1835.1835.1835.1835.1835.1835.1836.1839.1839.1839.1839.1839.1839.1839.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1841.1841.1841.1841.1841.1841.1841.1847.1847.1847.1847.1847.1847.1847.1847.1847.1847.1848.1848.1848.1848.1848.1848.1848.1848.1848.1848.1849.1849.1849.1869.1869.1869.1875.1875.1875.1895.1896.1896.1896.1896.1899.1899.1899.1899.1899.1899.1899.1899.1899.1899.1899.1899.1899.1899.1899.1899.1899.2204.2204.2204.2204.2204.2204.2204.2204.2204.2204.2208.2208.2208.2208.2211.2211.2211.2217.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2219.2255.2255.2255.2255.2255.2255.2255.2255.2255.2255.2257.2257.2258.2258.2258.2449.2449.2449.2449.2449.2449.2449.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2451.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2455.2455.2455.2455.2455.2457.2457.2457.2457.2457.2457.2457.2457.2458.2458.2459.2459.2459.2459.2459.2461.2461.2461.2461.2461.2461.2461.2461.2461.2461.2461.2461.2461.2486.2486.2486.2488.2488.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2679.2679.2682.2682.2682.2682.2682.2682.2684.2684.2685.2685.2685.2685.2685.2686.2686.2686.2686.2686.2686.2686.2686.2686.2686.2686.2687.2687.2687.2687.2687.2687.2687.2687.2687.2688.2688.2688.2688.3416.3416.3416.3418.3418.3418.3418.3420.3421.3421.3421.3421.3421.3421.3424.3424.3425.3426.3427.3427.3427.3427.3427.3427.3427.3427.3428.3428.3428.3428.3428.3428.3428.3428.3428.3428.3428.3428.3428.3428.3428.3428.3428.3428.3428.3429.3429.3429.3429.3429.3429.3429.3429.3429.3429.3429.3429.3429.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3430.3432.3432.3432.3435.3435.3435.3435.3436.3436.3440.3440.3440.3451.3451.3452.3452.3452.3452.3454.3455.3455.3457.3457.3457.3457.3457.3457.3457.3457.3457.3457.3457.3457.3457.3457.3457.3457.3457.3457.3459.3459.3459.3468.3468.3468.3468.3468.3468.3468.3468.3469.3470.3470.3471.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3472.3473.3473.3473.3473.3479.3479.3479.3479.3479.3479.3479.3481.3481.3481.3481.3481.3481.3483.3487.3487.3487.3487.3487.3488.3488.3488.3495.3495.3495.3495.3496.3496.3496.3496.3496.3497.3499.3499.3499.3499.3499.3499.3499.3499.3500.3500.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: 15 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15.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 we were asked to cook * CHA* *CHA* 22 we had to cook * C4D* we had to cook * ND * we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * NC * we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * NB * we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * NA * we had to cook * C1A* we had to cook * C2A* we had to cook * C3A* we had to cook * CMA* we had to cook * CAA* we had to cook * CBA* we had to cook * CGA* we had to cook * O2A* we had to cook * O1A* we had to cook * C2B* we had to cook * C3B* we had to cook * CAB* we had to cook * CBB* we had to cook * CMB* we had to cook * C2C* we had to cook * C3C* we had to cook * CAC* we had to cook * CBC* we had to cook * CMC* we had to cook * C2D* we had to cook * C3D* we had to cook * CAD* we had to cook * CBD* we had to cook * CGD* we had to cook * O2D* we had to cook * O1D* we had to cook * CMD* Creating DelPhi electrostatic grid real 0m27.929s user 0m25.397s sys 0m0.734s Adding spheres to tarted electrostatic grid we had to cook * NE2* we had to cook *HNE2* we had to cook *HNE1* we were asked to cook * CHA* *CHA* 22 we had to cook * C4D* we had to cook * ND * we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * NC * we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * NB * we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * NA * we had to cook * C1A* we had to cook * C2A* we had to cook * C3A* we had to cook * CMA* we had to cook * CAA* we had to cook * CBA* we had to cook * CGA* we had to cook * O2A* we had to cook * O1A* we had to cook * C2B* we had to cook * C3B* we had to cook * CAB* we had to cook * CBB* we had to cook * CMB* we had to cook * C2C* we had to cook * C3C* we had to cook * CAC* we had to cook * CBC* we had to cook * CMC* we had to cook * C2D* we had to cook * C3D* we had to cook * CAD* we had to cook * CBD* we had to cook * CGD* we had to cook * O2D* we had to cook * O1D* we had to cook * CMD* Creating DelPhi electrostatic grid real 0m28.142s user 0m25.402s sys 0m0.737s Creating box around spheres we were asked to cook * CHA* *CHA* 22 we had to cook * C4D* we had to cook * ND * we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * NC * we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * NB * we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * NA * we had to cook * C1A* we had to cook * C2A* we had to cook * C3A* we had to cook * CMA* we had to cook * CAA* we had to cook * CBA* we had to cook * CGA* we had to cook * O2A* we had to cook * O1A* we had to cook * C2B* we had to cook * C3B* we had to cook * CAB* we had to cook * CBB* we had to cook * CMB* we had to cook * C2C* we had to cook * C3C* we had to cook * CAC* we had to cook * CBC* we had to cook * CMC* we had to cook * C2D* we had to cook * C3D* we had to cook * CAD* we had to cook * CBD* we had to cook * CGD* we had to cook * O2D* we had to cook * O1D* we had to cook * CMD* Creating chemgrid maps real 0m25.279s user 0m24.526s sys 0m0.257s Atomic solvent excluded volume calculations underway FORTRAN STOP real 23m18.737s user 23m18.204s sys 0m0.042s Checking for WARNINGS in OUTPARM. WARNING--parameters not found for ATOM 4324 FE FE 2 sqrt(A), sqrt(B), and charge set to 0.0 WARNING--parameters not found for ATOM 4325 FE FE 3 sqrt(A), sqrt(B), and charge set to 0.0 Checking for WARNINGS in delphi.log. !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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 29 Number of atoms in ligand - 0 IL IS 3500 NR IS- 1 INTERNAL BEGUN INTERNAL COMPLETED 16 NUMLIG IS- 16 TOTAL NUMBER OF ORIENTATIONS WRITEN IS - 1 filtering complete mf7.csh - site preparation complete, preliminary docking queued