Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-09.c.bkslab.org du2 starts 1 molecule processed, 0 errors first try already in then inzinc count is 0 bzcat: Can't open input file 23: 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 23: 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 0m2.631s user 0m0.402s sys 0m0.191s 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 0:1291 spheres. 110. 110. 110. 110. 111. 111. 111. 111. 111. 111. 111. 111. 111. 111. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 127. 128. 128. 128. 128. 128. 128. 129. 129. 129. 129. 129. 129. 129. 130. 138. 138. 140. 140. 140. 140. 143. 147. 147. 147. 147. 147. 147. 147. 147. 372. 372. 372. 372. 376. 376. 376. 376. 376. 376. 376. 378. 378. 378. 378. 384. 384. 384. 384. 384. 386. 386. 386. 386. 386. 386. 391. 391. 391. 391. 391. 391. 391. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 397. 397. 397. 397. 397. 398. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 400. 400. 400. 400. 400. 400. 400. 400. 400. 401. 401. 401. 401. 401. 401. 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495. 495. 495. 495. 495. 495. 495. 495. 496. 498. 498. 498. 515. 515. 515. 515. 515. 515. 515. 515. 515. 515. 515. 515. 515. 529. 529. 783. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 798. 813. 814. 814. 823. 823. 823. 823. 823. 824. 824. 824. 824. 824. 824. 824. 831. 831. 831. 831. 831. 831. 831. 831. 831. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 896. 896. 899. 901. 901. 901. 901. 901. 901. 901. 901. 901. 902. 902. 902. 909. 909. 910. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912.1179.1179.1183.1183.1183.1183.1183.1183.1185.1185.1185.1187.1192.1198.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1209.1209.1209.1209.1210.1210.1210.1210.1212.1212.1212.1214.1215.1215.1215.1215.1216.1216.1216.1216.1217.1217.1217.1217.1217.1217.1218.1218.1218.1218.1218.1218.1218.1218.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1220.1220.1220.1220.1220.1220.1220.1220.1220.1220.1220.1220.1220.1229.1229.1229.1229.1253.1256.1256.1256.1256.1256.1256.1256.1256.1256.1256.1256.1425.1428.1429.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1433.1433.1434.1434.1434.1434.1434.1434.1434.1434.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1438.1438.1438.1439.1440.1440.1440.1440.1440.1440.1440.1440.1440.1444.1444.1444.1444.1444.1444.1446.1446.1446.1446.1455.1455.1455.1455.1455.1455.1455.1456.1456.1456.1456.1456.1456.1460.1460.1460.1460.1463.1463.1463.1463.1463.1463.1464.1654.1654.1657.1657.1657.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1677.1677.1677.1677.1677.1681.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1686.1687.1687.1840.1840.1840.1841.1841.1841.1841.1841.1841.1841.1841.1841.1841.1841.1841.1841.1841.1841.1841.1841.1842.1842.1842.1842.1842.1842.1842.1842.1844.1844.1844.1844.1856.1856.1856.1856.1856.1856.1856.1856.1856.1856.1856.1856.1857.1857.1857.1857.1857.1857.1857.1857.1857.1857.1857.1858.1858.1858.2068.2069.2069.2069.2074.2076.2076.2076.2076.2076.2086.2086.2086.2086.2086.2086.2086.2086.2087.2087.2087.2087.2087.2088.2088.2088.2088.2088.2088.2088.2088.2088.2088.2088.2088.2089.2089.2089.2089.2089.2089.2089.2089.2089.2089.2089.2089.2089.2089.2089.2089.2089.2091.2091.2091.2091.2091.2091.2091.2091.2091.2091.2091.2091.2091.2091.2093.2093.2093.2093.2093.2093.2093.2095.2095.2095.2095.2097.2099.2099.2099.2099.2099.2099.2102.2102.2104.2104.2104.2104.2104.2104.2105.2105.2105.2105.2105.2105.2105.2105.2107.2107.2107.2107.2107.2107.2107.2107.2107.2107.2107.2293.2293.2293.2293.2293.2293.2293.2293.2296.2296.2296.2296.2296.2296.2296.2296.2296.2302.2302.2302.2302.2302.2303.2303.2303.2303.2310.2310.2312.2312.2321.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: 37 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.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 0m27.594s user 0m25.565s sys 0m0.700s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m26.041s user 0m24.060s sys 0m0.544s Creating box around spheres Creating chemgrid maps real 0m23.297s user 0m22.526s sys 0m0.282s Atomic solvent excluded volume calculations underway FORTRAN STOP real 24m14.020s user 23m22.572s sys 0m0.201s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. File name = ../grids/distmap In source file scoreopt_so.f, at line number 625 PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. File name = ../grids/distmap In source file scoreopt_so.f, at line number 625 PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. File name = ../grids/distmap In source file scoreopt_so.f, at line number 625 not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar 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