Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-10.c.bkslab.org du2 starts 1 molecule processed, 0 errors first try already in then inzinc count is 0 nothing to compress count is 0 nothing to compress nothing to compress 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 2m43.289s user 0m0.681s sys 0m0.294s 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 0:1457 spheres. 75. 75. 112. 116. 116. 116. 116. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 119. 119. 120. 121. 121. 121. 122. 122. 123. 123. 123. 130. 133. 133. 133. 133. 133. 133. 134. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 136. 136. 136. 136. 137. 137. 137. 137. 137. 142. 143. 144. 145. 145. 145. 145. 145. 146. 147. 147. 147. 147. 147. 147. 148. 148. 148. 148. 148. 148. 148. 150. 150. 150. 150. 150. 150. 150. 150. 150. 150. 150. 150. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 168. 168. 168. 168. 168. 168. 168. 169. 171. 171. 171. 171. 171. 171. 171. 171. 175. 175. 178. 179. 179. 179. 179. 180. 180. 183. 189. 189. 189. 189. 189. 192. 194. 194. 194. 351. 351. 354. 354. 354. 354. 354. 354. 354. 355. 355. 355. 355. 355. 355. 355. 355. 355. 356. 356. 356. 356. 357. 357. 357. 357. 360. 360. 360. 360. 360. 379. 380. 380. 389. 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794. 803. 803. 803. 804. 804. 804. 804. 804. 809. 813. 813. 813. 817. 818. 818. 818. 818. 821. 821. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 824. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 832. 832. 832. 832. 832. 832. 833. 833. 834. 834. 834. 834. 834. 834. 834. 834. 834. 841. 841. 841. 844. 844. 844. 844. 844. 845. 848. 848. 848. 850. 850. 884.1176.1179.1179.1179.1179.1179.1179.1237.1242.1244.1244.1244.1246.1246.1246.1247.1247.1247.1247.1250.1250.1250.1252.1256.1256.1256.1256.1256.1256.1256.1270.1270.1270.1270.1270.1271.1271.1271.1271.1271.1271.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1273.1273.1275.1275.1275.1275.1275.1275.1275.1275.1275.1276.1276.1276.1276.1276.1276.1276.1277.1277.1277.1277.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1279.1280.1280.1280.1280.1280.1280.1280.1280.1285.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1287.1287.1287.1287.1289.1290.1290.1290.1290.1293.1293.1293.1293.1293.1293.1293.1293.1293.1295.1295.1295.1296.1304.1304.1309.1309.1309.1309.1309.1309.1309.1309.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1328.1329.1329.1358.1358.1358.1358.1358.1364.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1379.1379.1379.1379.1379.1381.1381.1381.1381.1384.1384.1389.1389.1389.1389.1389.1390.1391.1391.1391.1682.1682.1722.1723.1723.1723.1723.1723.1723.1725.1725.1725.1725.1725.1725.1726.1726.1726.1726.1728.1728.1728.1730.1730.1730.1730.1730.1731.1731.1731.1731.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1733.1733.1733.1733.1733.1733.1733.1740.1740.1740.1740.1740.1741.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1743.1743.1743.1743.1743.1743.1743.1743.1743.1744.1744.1744.1747.1752.1752.1752.1752.1752.1752.1754.1754.1754.1754.1754.1754.1754.1755.1755.1755.1755.1755.1756.1756.1756.1757.1757.1757.1757.1757.1757.1757.1757.1757.1757.1757.1757.1757.1760.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1774.1775.1775.1775.1775.1775.1775.1775.1775.1775.1775.1776.1776.1778.1778.1778.1778.1778.1779.1782.1782.1783.1783.1783.1785.1785.1785.1785.1785.1785.1785.1787.1787.1787.1790.1790.1792.1792.1792.1793.1793.1793.1793.1796.1796.1796.1801.1956.1956.1958.1959.1959.1960.1960.1960.1960.1960.1960.1960.1960.1960.1960.1961.1961.1966.1967.1967.1967.1967.1967.1984.1985.1985.1985.1985.1985.1985.1992.1992.2021.2021.2021.2023.2023.2023.2023.2023.2044.2044.2044.2044.2045.2045.2045.2045.2045.2045.2045.2045.2045.2045.2045.2045.2045.2045.2053.2053.2053.2053.2053.2053.2053.2053.2055.2055.2055.2055.2055.2056.2058.2058.2062.2063.2064.2064.2064.2064.2065.2065.2065.2066.2066.2067.2067.2067.2067.2069.2069.2069.2070.2070.2076.2076.2076.2076.2076.2077.2077.2077.2077.2078.2078.2078.2078.2078.2078.2078.2078.2078.2078.2078.2078.2081.2081.2081.2081.2103.2103.2103.2112.2319.2319.2319.2319.2321.2321.2321.2321.2321.2321.2321.2325.2327.2327.2327.2327.2328.2328.2331.2331.2332.2332.2332.2332.2333.2334.2334.2334.2334.2334.2334.2334.2334.2335.2335.2339.2339.2340.2340.2340.2341.2341.2342.2349.2349.2351.2351.2351.2351.2351.2351.2351.2351.2359.2359.2359.2360.2360.2360.2363.2363.2363.2363.2363.2363.2366.2366.2366.2366.2366.2366.2366.2366.2366.2366.2366.2371.2371.2371.2374.2374.2374.2374.2374.2374.2374.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2376.2376.2376.2376.2376.2380.2380.2380.2380.2380.2380.2381.2381.2381.2381.2381.2381.2381.2382.2382.2382.2382.2382.2382.2382.2382.2382.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2391.2391.2391.2393.2394.2394.2395.2395.2397.2398.2398.2398.2398.2398.2398.2407.2407.2408.2408.2408.2409.2409.2409.2417.2422.2422.2422.2424.2427.2427.2427.2427.2427.2427.2427.2427.2427.2427.2427.2427.2427.2427.2428.2428.2429.2429.2429.2429.2429.2429.2429.2429.2429.2430.2432.2432.2436.2436.2436.2436.2436.2436.2436.2436.2436.2436.2436.2437.2437.2437.2437.2437.2437.2437.2438.2438.2438.2438.2438.2438.2438.2438.2438.2438.2438.2438.2438.2448.2448.2448.2452.2452.2452.2455.2488.2488.2488.2488.2488.2488.2488.2488.2488.2494.2815.2815.2819.2819.2819.2819.2819.2819.2819.2841.2841.2846.2846.2846.2848.2848.2850.2850.2850.2850.2850.2850.2850.2851.2851.2851.2852.2853.2854.2856.2860.2860.2860.2860.2860.2860.2860.2860.2874.2875.2875.2875.2875.2875.2875.2875.2876.2876.2876.2876.2876.2876.2876.2876.2876.2876.2878.2879.2879.2879.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2881.2881.2881.2881.2881.2881.2882.2882.2882.2882.2882.2882.2882.2882.2882.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2893.2894.2895.2895.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2900.2900.2900.2900.2900.2900.2900.2913.2913.2913.2922.2922.2922.2922.2922.2922.2929.2932.2932.2932.2933.2933.2933.2933.2933.2933.2933.2962.2962.2962.2962.2964.2968.2968.2969.2969.2969.2970.2981.2981.2981.2981.2981.2981.2981.2981.2981.2983.2983.2983.2983.2983.2985.2988.2993.2993.2993.2993.2993.2993.2995.2995.2995.2997.2997.2997.2997.2997.2997.2997.2997.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: 58 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. 25. 26. 27. 28. 29. 30. 31. 32. 33. 34. 35. 36. 37. 38. 39. 40. 41. 42. 43. 44. 45. 46. 47. 48. 49. 50. 51. 52. 53. 54. 55. 56. 57. 58.FORTRAN STOP Adding essential hydrogens to receptor #@jens_hydrogens.csh rec.pdb 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 had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * Creating DelPhi electrostatic grid real 1m42.967s user 0m21.433s sys 0m0.557s Adding spheres to tarted electrostatic grid we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * Creating DelPhi electrostatic grid real 1m30.743s user 0m20.633s sys 0m0.495s Creating box around spheres we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * we had to cook * HA * Creating chemgrid maps real 0m48.460s user 0m14.773s sys 0m0.162s Atomic solvent excluded volume calculations underway FORTRAN STOP real 79m37.643s user 27m45.970s sys 0m0.095s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. Stop before docking.