Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-12.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 48: No such file or directory. bzcat: Can't open input file 03: 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 48: No such file or directory. bzcat: Can't open input file 03: 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 0m3.131s user 0m0.490s sys 0m0.313s 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 0:1246 spheres. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 425. 425. 425. 425. 425. 425. 435. 436. 436. 436. 436. 437. 437. 437. 437. 437. 437. 437. 438. 438. 438. 438. 438. 440. 440. 442. 442. 442. 442. 442. 442. 442. 442. 442. 442. 442. 442. 442. 442. 442. 442. 442. 442. 453. 453. 453. 453. 453. 453. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 457. 484. 484. 484. 484. 484. 484. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 486. 487. 487. 487. 487. 487. 487. 519. 519. 519. 519. 519. 519. 519. 519. 519. 766. 766. 772. 775. 775. 775. 775. 775. 776. 776. 776. 776. 776. 776. 777. 777. 777. 777. 777. 785. 786. 786. 786. 786. 786. 786. 787. 787. 934. 934. 934. 935. 937. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 939. 939. 939. 939. 939. 939. 943. 943. 943. 943. 943. 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976.1071.1081.1081.1081.1082.1082.1082.1082.1082.1082.1082.1082.1083.1083.1083.1083.1083.1089.1089.1090.1090.1090.1628.1632.1636.1637.1637.1637.1637.1637.1644.1644.1644.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1646.1646.1646.1646.1646.1646.1646.1648.1658.1658.1658.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1659.1663.1663.1663.1663.1667.1667.1667.1667.1667.1667.1667.1667.1667.1667.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1669.1670.1670.1670.1670.1670.1670.1670.1670.1671.1671.1671.1671.1671.1671.1671.1672.1672.1672.1672.1672.1672.1672.1672.1673.1673.1673.1674.1674.1764.1767.1767.1781.1781.1783.1783.1783.1783.1784.1788.1792.1804.1805.1805.1805.1807.1807.1807.1807.1807.1807.1807.1807.1807.1807.1807.1807.1807.1807.1807.1807.1808.1809.1809.1810.1810.1814.1819.1819.1819.1819.1821.1829.1829.1829.1829.1829.1829.1829.1829.1829.1829.1829.1829.1829.1829.1829.1829.1829.1831.1831.1831.1831.1831.1831.1831.1831.1831.1831.1831.1831.1831.1831.1831.1831.1831.1832.1832.1832.1839.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1840.1842.1842.1842.1842.1845.1845.1845.1845.1845.1845.1845.1845.1845.1846.1846.1846.1846.1846.1846.1846.1846.1846.1846.1847.1847.1847.1848.1848.1848.1848.1848.1848.1848.1848.1848.1848.1848.1848.1848.1848.1848.1848.1848.1849.1849.1865.1865.1865.1865.1865.1865.1865.1865.1865.1865.1865.1865.1865.1865.1865.1865.1865.1865.1867.1867.1867.1867.1873.1873.1873.1873.1873.1873.1873.1873.1874.1874.1877.1877.1877.1877.1877.1877.1877.1877.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1878.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1879.1885.1885.1885.1885.1885.1885.1885.1885.1886.1886.1886.1886.1886.1886.1886.1886.1887.1887.1887.1887.1887.1887.1887.1912.1912.1912.1913.1913.1913.1934.1934.1937.1937.1937.1937.1937.1937.1937.1937.1937.1937.1937.1937.1937.1937.2237.2239.2239.2242.2242.2242.2242.2242.2249.2249.2249.2249.2249.2249.2249.2249.2252.2255.2255.2255.2255.2255.2255.2255.2256.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2293.2293.2293.2293.2293.2293.2293.2293.2293.2293.2293.2293.2295.2296.2296.2296.2296.2296.2296.2487.2487.2487.2487.2487.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2492.2492.2492.2492.2492.2492.2492.2492.2492.2492.2492.2492.2492.2493.2493.2493.2494.2495.2495.2495.2495.2495.2495.2495.2496.2496.2496.2496.2496.2497.2497.2497.2497.2497.2497.2498.2498.2498.2498.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2523.2524.2524.2525.2525.2525.2525.2525.2526.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2528.2696.2696.2696.2696.2696.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2699.2717.2717.2717.2720.2720.2720.2720.2722.2722.2723.2723.2723.2723.2723.2723.2723.2724.2724.2724.2724.2724.2724.2724.2724.2724.2724.2725.2725.2725.2725.2725.2725.2725.2725.2726.2726.2726.3443.3443.3443.3444.3444.3447.3447.3450.3450.3450.3452.3452.3453.3453.3453.3453.3453.3453.3453.3453.3453.3453.3453.3454.3454.3454.3454.3454.3454.3454.3454.3454.3454.3454.3454.3455.3455.3455.3455.3455.3455.3455.3455.3455.3455.3455.3455.3455.3455.3455.3455.3455.3455.3455.3455.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3456.3457.3457.3460.3460.3460.3461.3464.3464.3474.3474.3474.3475.3475.3475.3476.3476.3477.3477.3478.3480.3480.3480.3480.3480.3480.3480.3480.3480.3480.3480.3480.3480.3480.3482.3482.3484.3486.3494.3494.3494.3494.3494.3495.3496.3496.3496.3498.3498.3498.3498.3498.3498.3498.3498.3498.3498.3498.3498.3498.3498.3498.3498.3498.3498.3499.3499.3499.3499.3499.3499.3499.3499.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3504.3506.3506.3506.3506.3506.3511.3511.3511.3511.3512.3512.3512.3512.3512.3514.3518.3518.3518.3518.3519.3519.3519.3519.3519.3520.3520.3520.3520.3522.3522.3522.3522.3522.3523.3523.3523.3523.3523.3523.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: 16 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16.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 0m26.809s user 0m21.490s sys 0m0.553s 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 0m25.254s user 0m21.458s sys 0m0.566s 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 0m23.941s user 0m23.175s sys 0m0.203s Atomic solvent excluded volume calculations underway FORTRAN STOP real 24m53.047s user 24m52.394s sys 0m0.097s Checking for WARNINGS in OUTPARM. WARNING--parameters not found for ATOM 4270 FE HEM 819 sqrt(A), sqrt(B), and charge set to 0.0 -- WARNING--parameters not found for ATOM 4358 FE FE 3 sqrt(A), sqrt(B), and charge set to 0.0 Checking for WARNINGS in delphi.log. !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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