Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-2-41.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. 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 22: No such file or directory. bzcat: Can't open input file 26: 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 22: No such file or directory. bzcat: Can't open input file 26: 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 0m3.664s user 0m0.586s sys 0m0.505s 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 0:1214 spheres. 375. 375. 376. 378. 378. 378. 380. 380. 380. 380. 380. 380. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 382. 393. 393. 393. 393. 393. 393. 393. 393. 394. 394. 397. 397. 397. 397. 397. 397. 397. 397. 397. 397. 423. 423. 424. 424. 424. 424. 424. 424. 424. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 426. 427. 427. 427. 427. 427. 427. 427. 427. 427. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 621. 621. 621. 699. 705. 708. 708. 708. 708. 708. 708. 708. 708. 708. 709. 709. 709. 709. 709. 709. 709. 710. 710. 710. 718. 719. 719. 719. 720. 720. 720. 860. 860. 860. 860. 860. 860. 860. 860. 860. 860. 860. 860. 860. 860. 860. 860. 863. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 864. 865. 865. 865. 869. 869. 869. 869. 869. 872. 872. 872. 872. 872. 872. 872. 872. 872. 872. 872. 872. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 874. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 878. 881. 883. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 891. 895. 895. 895. 895. 895. 897. 899. 899. 900. 900. 901. 901. 901. 901. 901. 901. 901. 901. 901. 901. 901. 901. 901. 901. 901. 901. 901. 902. 906. 989.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1001.1001.1001.1001.1001.1007.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1550.1550.1555.1555.1562.1562.1563.1563.1563.1563.1563.1563.1563.1563.1563.1563.1563.1563.1563.1563.1563.1563.1564.1564.1564.1564.1564.1564.1576.1576.1576.1576.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1577.1580.1580.1580.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1581.1585.1585.1585.1585.1585.1585.1585.1585.1585.1585.1585.1587.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1588.1589.1590.1590.1590.1590.1591.1591.1591.1591.1591.1591.1591.1591.1591.1591.1591.1591.1591.1591.1591.1591.1591.1591.1591.1591.1592.1596.1599.1599.1599.1599.1599.1599.1599.1599.1599.1599.1699.1699.1700.1700.1700.1701.1701.1701.1705.1710.1710.1722.1725.1725.1725.1725.1725.1725.1725.1725.1725.1725.1726.1726.1727.1727.1727.1737.1737.1737.1737.1737.1739.1739.1739.1747.1747.1747.1747.1747.1747.1747.1747.1747.1747.1747.1747.1747.1747.1747.1749.1749.1749.1749.1749.1749.1749.1750.1750.1750.1750.1757.1758.1758.1758.1758.1758.1758.1758.1758.1758.1758.1758.1758.1758.1760.1760.1760.1760.1760.1763.1763.1763.1763.1763.1763.1763.1763.1763.1764.1764.1764.1764.1764.1764.1764.1764.1764.1764.1764.1764.1765.1765.1766.1766.1766.1766.1766.1766.1766.1766.1766.1766.1766.1767.1767.1783.1783.1783.1783.1783.1783.1783.1783.1783.1783.1783.1783.1783.1783.1783.1783.1783.1783.1783.1791.1791.1791.1791.1791.1791.1791.1791.1791.1795.1795.1795.1795.1795.1795.1795.1795.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1796.1797.1797.1797.1797.1797.1797.1797.1797.1797.1797.1797.1797.1797.1797.1797.1797.1797.1797.1803.1803.1803.1803.1803.1803.1803.1803.1804.1804.1804.1804.1804.1804.1804.1804.1804.1804.1805.1805.1805.1825.1831.1852.1852.1852.1852.1852.1852.1855.1855.1855.1855.1855.1855.1855.1855.1855.1855.1855.1855.1855.1855.1855.1855.1855.1855.1856.2160.2160.2160.2160.2160.2160.2160.2160.2164.2164.2167.2167.2167.2167.2170.2171.2173.2173.2173.2175.2175.2175.2175.2175.2175.2175.2175.2175.2175.2175.2175.2175.2175.2175.2175.2175.2211.2211.2211.2211.2211.2214.2214.2214.2405.2405.2405.2405.2405.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2407.2410.2410.2410.2410.2410.2410.2410.2410.2410.2410.2410.2410.2410.2410.2410.2410.2410.2410.2410.2410.2411.2411.2411.2411.2413.2413.2413.2413.2413.2413.2413.2413.2413.2413.2414.2414.2415.2415.2415.2415.2415.2415.2415.2415.2415.2415.2415.2415.2415.2415.2415.2417.2417.2417.2417.2417.2417.2417.2417.2417.2417.2417.2417.2417.2417.2417.2442.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2445.2446.2446.2446.2446.2446.2446.2446.2446.2446.2446.2446.2446.2635.2638.2638.2638.2638.2639.2639.2640.2640.2641.2641.2641.2641.2641.2641.2642.2642.2642.2642.2642.2643.2643.2643.2643.2643.2643.2643.2644.2644.2644.2644.2644.2644.2644.2644.3366.3368.3368.3370.3370.3370.3370.3370.3370.3370.3373.3373.3375.3376.3376.3376.3376.3376.3376.3376.3376.3377.3377.3377.3377.3377.3377.3377.3377.3377.3377.3377.3377.3377.3377.3377.3378.3378.3378.3378.3378.3378.3378.3378.3378.3378.3378.3378.3378.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3379.3380.3380.3380.3380.3380.3383.3383.3383.3387.3397.3397.3397.3398.3398.3398.3398.3398.3398.3401.3401.3401.3403.3403.3403.3403.3403.3403.3403.3403.3403.3403.3403.3403.3403.3404.3405.3409.3409.3417.3417.3417.3417.3417.3417.3417.3417.3417.3417.3417.3417.3417.3417.3417.3417.3419.3419.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3421.3422.3422.3422.3422.3422.3427.3427.3427.3427.3427.3427.3427.3427.3427.3427.3427.3427.3427.3427.3427.3427.3427.3427.3429.3429.3429.3429.3429.3434.3434.3434.3434.3434.3435.3437.3440.3441.3441.3441.3441.3441.3441.3441.3442.3442.3442.3442.3443.3443.3443.3445.3445.3445.3445.3445.3445.3446.3446.3446.3450.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: 13 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13.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 * C3D* we had to cook * C2D* we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * C3C* we had to cook * C2C* we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * C3B* we had to cook * C2B* we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * C3A* we had to cook * C2A* we had to cook * C1A* we had to cook * NA * 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 * CMA* we had to cook * NB * we had to cook * CMB* we had to cook * CAB* we had to cook * CBB* we had to cook * NC * we had to cook * CMC* we had to cook * CAC* we had to cook * CBC* we had to cook * ND * we had to cook * CMD* 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* Creating DelPhi electrostatic grid real 0m37.227s user 0m33.304s sys 0m1.423s 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 * C3D* we had to cook * C2D* we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * C3C* we had to cook * C2C* we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * C3B* we had to cook * C2B* we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * C3A* we had to cook * C2A* we had to cook * C1A* we had to cook * NA * 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 * CMA* we had to cook * NB * we had to cook * CMB* we had to cook * CAB* we had to cook * CBB* we had to cook * NC * we had to cook * CMC* we had to cook * CAC* we had to cook * CBC* we had to cook * ND * we had to cook * CMD* 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* Creating DelPhi electrostatic grid real 0m38.742s user 0m33.419s sys 0m1.383s Creating box around spheres we were asked to cook * CHA* *CHA* 22 we had to cook * C4D* we had to cook * C3D* we had to cook * C2D* we had to cook * C1D* we had to cook * CHD* we had to cook * C4C* we had to cook * C3C* we had to cook * C2C* we had to cook * C1C* we had to cook * CHC* we had to cook * C4B* we had to cook * C3B* we had to cook * C2B* we had to cook * C1B* we had to cook * CHB* we had to cook * C4A* we had to cook * C3A* we had to cook * C2A* we had to cook * C1A* we had to cook * NA * 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 * CMA* we had to cook * NB * we had to cook * CMB* we had to cook * CAB* we had to cook * CBB* we had to cook * NC * we had to cook * CMC* we had to cook * CAC* we had to cook * CBC* we had to cook * ND * we had to cook * CMD* 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* Creating chemgrid maps real 1m33.958s user 1m32.726s sys 0m0.467s Atomic solvent excluded volume calculations underway FORTRAN STOP real 24m5.576s user 24m4.550s sys 0m0.126s Checking for WARNINGS in OUTPARM. WARNING--parameters not found for ATOM 4181 FE HEM 818 sqrt(A), sqrt(B), and charge set to 0.0 WARNING--parameters not found for ATOM 4267 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 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 !!! WARNING: HEM 818 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 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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