Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-05.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 17: No such file or directory. bzcat: Can't open input file 86: 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 17: No such file or directory. bzcat: Can't open input file 86: 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 0m2.256s user 0m0.399s sys 0m0.254s 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 0:1372 spheres. 387. 387. 439. 443. 443. 443. 444. 444. 444. 444. 444. 444. 444. 444. 444. 444. 444. 444. 445. 445. 445. 445. 445. 445. 445. 445. 447. 447. 447. 447. 447. 447. 447. 447. 447. 451. 451. 451. 451. 455. 455. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 457. 457. 457. 457. 457. 457. 457. 457. 457. 462. 462. 462. 463. 463. 463. 463. 463. 464. 464. 464. 464. 464. 465. 465. 465. 465. 465. 465. 465. 465. 465. 465. 465. 465. 491. 491. 492. 492. 492. 492. 492. 492. 492. 492. 492. 492. 492. 492. 492. 492. 492. 492. 495. 497. 497. 497. 499. 500. 774. 774. 774. 774. 775. 775. 775. 775. 775. 775. 775. 776. 776. 776. 776. 796. 796. 796. 796. 801. 801. 801. 801. 801. 801. 801. 802. 806. 806. 811. 812. 813. 813. 813. 813. 815. 815. 816. 816. 816. 816. 816. 819. 819. 819. 819. 819. 819. 819. 819. 822. 822. 822. 822. 822. 822. 822. 822. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 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832.1004.1004.1004.1004.1004.1004.1004.1004.1004.1004.1004.1004.1247.1247.1247.1247.1247.1247.1247.1249.1249.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1252.1252.1253.1253.1253.1254.1254.1254.1254.1254.1254.1254.1255.1255.1255.1256.1256.1256.1264.1265.1265.1265.1265.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1270.1271.1271.1271.1271.1271.1271.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1273.1273.1273.1273.1273.1273.1273.1273.1275.1277.1277.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1281.1281.1281.1283.1283.1283.1283.1283.1283.1284.1285.1286.1288.1288.1288.1288.1288.1288.1288.1288.1288.1298.1298.1298.1298.1298.1298.1305.1305.1305.1305.1305.1305.1305.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1545.1549.1549.1549.1549.1549.1549.1549.1549.1549.1550.1550.1550.1550.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1555.1559.1561.1561.1561.1561.1561.1561.1561.1561.1561.1561.1561.1561.1561.1561.1561.1561.1561.1561.1561.1561.1565.1567.1567.1567.1567.1567.1567.1567.1568.1568.1568.1568.1568.1569.1569.1569.1569.1569.1569.1569.1569.1569.1571.1571.1573.1574.1574.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1582.1582.1582.1582.1582.1582.1582.1582.1582.1582.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1583.1585.1585.1585.1585.1585.1585.1585.1585.1585.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1593.1593.1596.1599.1599.1600.1600.1600.1600.1600.1602.1602.1602.1657.1657.1657.1665.1665.1668.1671.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1672.1673.1675.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1677.1677.1677.1677.1677.1677.1677.1677.1677.1677.1683.1683.1684.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1685.1687.1689.1694.1694.1694.1695.1695.1695.1695.1695.1695.1695.1696.1696.1696.1696.1696.1697.1698.1698.1698.1698.1698.1698.1698.1698.1699.1699.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1706.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1713.1713.1713.1713.1713.1713.1713.1714.1714.1714.1714.1714.1714.1714.1714.1716.1716.1716.1716.1719.1719.1719.1719.1719.1719.1719.1719.1719.1719.1719.1719.1719.1719.1719.1728.1729.1729.1730.1730.1730.1730.1730.1730.1730.1730.1730.1742.1742.1742.1742.1742.1743.1743.1743.1743.1743.1743.1744.1744.1744.1744.1744.1744.1744.1745.1745.1745.1745.1745.1745.1745.1745.1745.1745.1745.1745.1745.1745.1745.1745.1745.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1746.1766.1767.1767.1767.1770.1773.1774.1774.1774.1774.1883.1887.1887.1887.1887.1887.1887.1888.1888.1888.1889.1889.1889.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1890.1894.1894.1894.1895.1895.1895.1895.1895.1895.1895.1895.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1897.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1898.1904.1904.1904.1904.1904.1904.1904.1905.1905.1905.1906.1906.1906.1962.1962.1965.1965.1965.1965.1965.1965.1966.1966.1966.1966.1967.1967.1967.1967.1967.1967.1967.1967.1967.1968.1968.1969.1969.1969.1969.1969.1969.1969.1969.1975.1976.1976.1976.1976.1976.1976.1976.1976.1977.1977.1977.1982.1983.1983.1983.1983.1983.1983.1983.1983.1983.1984.1986.1986.1986.1989.1989.1989.1989.1989.1989.1989.1989.1989.1989.1989.1989.1989.1989.1989.1989.1990.1990.1990.1992.1994.1994.1994.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1995.1996.1996.1996.1996.1996.1996.1996.1996.1996.1996.1997.1997.1998.1998.1998.1998.1998.1998.1998.1998.1998.1998.2005.2005.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2006.2007.2012.2013.2013.2013.2013.2013.2013.2013.2013.2013.2016.2016.2016.2016.2016.2017.2017.2017.2020.2020.2020.2023.2023.2023.2023.2023.2023.2023.2023.2023.2023.2023.2023.2024.2024.2024.2024.2025.2025.2025.2025.2025.2025.2025.2025.2025.2025.2025.2025.2025.2025.2025.2025.2025.2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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: 24 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.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 0m24.506s user 0m21.189s sys 0m0.619s 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 0m25.278s user 0m21.627s sys 0m0.572s Creating box around spheres Creating chemgrid maps real 0m19.525s user 0m18.773s sys 0m0.248s Atomic solvent excluded volume calculations underway FORTRAN STOP real 28m19.413s user 28m18.701s sys 0m0.184s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar failed to get similars