Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-09.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 3m30.339s user 0m0.551s sys 0m0.370s 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 0:1345 spheres. 138. 138. 138. 138. 138. 138. 138. 139. 140. 140. 140. 140. 140. 140. 140. 140. 140. 140. 140. 140. 140. 140. 140. 140. 140. 140. 141. 141. 141. 141. 141. 141. 141. 141. 141. 141. 142. 142. 142. 142. 142. 142. 142. 143. 150. 150. 150. 150. 150. 150. 150. 150. 152. 152. 152. 152. 152. 153. 153. 153. 153. 153. 153. 154. 154. 154. 154. 154. 154. 154. 154. 154. 154. 154. 163. 163. 163. 163. 163. 163. 163. 163. 163. 173. 173. 173. 173. 173. 173. 173. 173. 173. 176. 176. 176. 176. 176. 176. 176. 176. 177. 177. 177. 177. 180. 183. 183. 184. 184. 184. 186. 188. 188. 188. 372. 383. 383. 383. 383. 383. 383. 419. 419. 419. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 421. 443. 443. 443. 443. 443. 443. 443. 443. 443. 443. 443. 451. 451. 451. 451. 451. 451. 451. 451. 451. 453. 453. 453. 453. 453. 456. 456. 460. 460. 460. 461. 461. 461. 461. 461. 462. 462. 462. 462. 462. 464. 464. 464. 464. 464. 464. 464. 464. 464. 464. 464. 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827. 827. 827. 827. 827. 827. 827. 827. 827. 828. 828. 833. 834. 834. 834. 834. 834. 834. 834. 834. 835. 835. 835. 835. 835. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 836. 843. 843. 843. 843. 843. 843. 843. 843. 846. 850. 850. 850. 850. 850. 853. 886. 921. 924. 925. 925. 925. 925. 925. 931. 931. 931. 931. 931. 934.1172.1172.1174.1174.1177.1177.1177.1177.1177.1180.1243.1243.1247.1247.1247.1247.1248.1248.1248.1251.1253.1257.1269.1270.1270.1270.1270.1271.1271.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1273.1273.1273.1273.1273.1273.1273.1273.1273.1276.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1278.1278.1278.1278.1278.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1280.1280.1281.1283.1287.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1288.1290.1291.1291.1293.1293.1293.1295.1295.1295.1295.1295.1295.1295.1295.1295.1295.1295.1297.1297.1297.1297.1297.1297.1303.1306.1317.1319.1319.1319.1319.1319.1319.1319.1319.1324.1326.1329.1329.1329.1329.1329.1359.1365.1365.1366.1367.1378.1378.1378.1378.1378.1378.1378.1378.1379.1379.1379.1379.1382.1382.1384.1385.1385.1385.1385.1385.1385.1386.1386.1390.1390.1390.1390.1390.1390.1391.1392.1392.1392.1392.1392.1392.1392.1393.1428.1702.1702.1704.1705.1705.1705.1705.1705.1705.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1707.1708.1708.1708.1708.1708.1708.1708.1708.1708.1709.1709.1709.1709.1709.1717.1719.1719.1719.1719.1719.1719.1719.1720.1720.1720.1720.1720.1721.1721.1721.1721.1721.1721.1721.1721.1721.1721.1730.1730.1730.1740.1740.1740.1740.1740.1743.1743.1743.1743.1743.1743.1750.1751.1751.1751.1751.1950.1950.1986.1988.1988.1988.1988.1988.1988.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2010.2018.2018.2018.2018.2018.2018.2020.2020.2020.2020.2020.2023.2023.2023.2023.2023.2027.2027.2028.2028.2028.2029.2029.2029.2029.2029.2029.2029.2029.2029.2029.2029.2029.2030.2030.2031.2031.2031.2031.2031.2031.2031.2031.2031.2031.2031.2031.2031.2031.2031.2031.2031.2031.2032.2032.2032.2034.2034.2034.2035.2041.2041.2041.2042.2042.2042.2042.2042.2042.2042.2042.2042.2043.2055.2068.2068.2068.2068.2068.2068.2280.2280.2286.2286.2286.2286.2286.2296.2296.2297.2298.2298.2298.2298.2298.2298.2298.2298.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2299.2300.2300.2303.2304.2304.2304.2304.2304.2306.2306.2307.2307.2307.2307.2308.2308.2308.2308.2308.2308.2309.2314.2314.2314.2316.2319.2319.2324.2324.2324.2325.2325.2327.2328.2328.2328.2334.2334.2337.2337.2338.2338.2339.2339.2339.2339.2339.2339.2339.2339.2339.2339.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2340.2341.2341.2341.2341.2341.2341.2343.2343.2345.2345.2345.2345.2345.2345.2345.2345.2345.2345.2346.2347.2347.2347.2349.2349.2349.2349.2349.2349.2349.2349.2349.2349.2351.2352.2352.2354.2354.2354.2356.2358.2358.2359.2359.2359.2361.2361.2361.2361.2361.2361.2362.2372.2372.2372.2373.2373.2373.2373.2373.2373.2376.2377.2378.2378.2378.2378.2382.2382.2382.2382.2382.2386.2386.2387.2387.2387.2387.2390.2391.2391.2391.2392.2392.2392.2392.2392.2392.2392.2392.2392.2392.2392.2392.2392.2392.2393.2393.2393.2393.2393.2393.2393.2393.2393.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2394.2397.2397.2397.2401.2401.2401.2401.2402.2402.2402.2402.2402.2402.2402.2402.2402.2403.2403.2403.2403.2403.2403.2403.2405.2405.2410.2413.2413.2418.2418.2418.2418.2426.2427.2430.2431.2431.2431.2431.2432.2432.2434.2435.2435.2437.2440.2440.2440.2441.2441.2441.2441.2441.2441.2441.2441.2446.2484.2484.2484.2494.2494.2494.2494.2494.2494.2494.2494.2732.2732.2732.2732.2734.2734.2734.2734.2734.2734.2735.2735.2737.2737.2737.2737.2737.2737.2740.2740.2740.2740.2774.2780.2798.2803.2803.2803.2803.2803.2807.2807.2808.2808.2808.2808.2808.2808.2808.2808.2808.2809.2811.2811.2811.2811.2813.2831.2831.2831.2832.2832.2832.2832.2832.2832.2832.2832.2832.2832.2832.2832.2832.2832.2832.2832.2832.2832.2832.2833.2836.2836.2836.2836.2836.2836.2836.2836.2836.2837.2837.2837.2837.2837.2837.2837.2837.2837.2837.2837.2837.2837.2837.2837.2837.2837.2837.2846.2847.2847.2847.2847.2847.2847.2847.2847.2847.2847.2847.2847.2847.2847.2848.2848.2848.2848.2848.2848.2848.2851.2851.2851.2851.2851.2851.2851.2853.2853.2853.2853.2855.2855.2856.2866.2866.2866.2879.2879.2879.2879.2889.2889.2889.2889.2889.2890.2890.2925.2926.2926.2926.2938.2938.2938.2938.2938.2938.2938.2938.2939.2939.2939.2942.2944.2945.2945.2945.2945.2945.2946.2946.2946.2950.2950.2950.2950.2950.2950.2951.2952.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: 66 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. 59. 60. 61. 62. 63. 64. 65. 66.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 * Creating DelPhi electrostatic grid real 1m18.974s user 0m24.836s sys 0m0.704s 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 * Creating DelPhi electrostatic grid real 1m50.690s user 0m26.239s sys 0m0.727s 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 * Creating chemgrid maps real 0m35.377s user 0m10.066s sys 0m0.239s Atomic solvent excluded volume calculations underway FORTRAN STOP real 51m14.464s user 17m15.421s sys 0m0.109s 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.