Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-14.c.bkslab.org du2 starts 1 molecule processed, 0 errors convert.py (MDL SDF -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 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 68: No such file or directory. bzcat: Can't open input file 61: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. count is 0 bzcat: Can't open input file 72: No such file or directory. bzcat: Can't open input file 16: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. bzcat: Can't open input file 68: No such file or directory. bzcat: Can't open input file 61: No such file or directory. bzcat: Can't open input file 72: No such file or directory. bzcat: Can't open input file 16: No such file or directory. 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 0m2.340s user 0m0.325s sys 0m0.168s 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: 660 spheres. 110. 110. 110. 111. 111. 111. 111. 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. 128. 128. 128. 128. 128. 129. 129. 129. 130. 130. 130. 130. 130. 136. 136. 137. 138. 138. 138. 138. 138. 141. 141. 143. 143. 143. 143. 143. 143. 143. 143. 143. 143. 143. 143. 143. 143. 143. 146. 379. 379. 379. 379. 379. 417. 417. 417. 417. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 421. 421. 421. 421. 422. 428. 428. 428. 428. 428. 434. 435. 435. 449. 449. 449. 449. 449. 451. 451. 451. 451. 451. 451. 451. 455. 458. 458. 458. 458. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 463. 463. 463. 463. 463. 464. 464. 464. 464. 464. 464. 464. 464. 464. 464. 464. 471. 471. 471. 471. 471. 471. 471. 471. 472. 472. 472. 472. 472. 473. 473. 480. 480. 481. 481. 484. 484. 484. 484. 484. 484. 484. 484. 484. 488. 488. 488. 488. 488. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 490. 490. 490. 490. 490. 491. 491. 491. 492. 492. 492. 492. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 781. 781. 781. 781. 788. 788. 788. 788. 788. 788. 788. 792. 792. 792. 792. 792. 792. 795. 811. 811. 811. 821. 821. 821. 821. 821. 821. 821. 821. 821. 821. 822. 822. 822. 822. 822. 822. 822. 822. 822. 896. 896. 896. 896. 896. 896. 896. 897. 897. 899. 899. 899. 899. 899. 906. 906. 908. 908. 908. 909. 909. 909. 909. 909. 909. 909. 909.1191.1191.1191.1191.1191.1191.1191.1193.1193.1193.1193.1194.1194.1194.1194.1194.1194.1194.1194.1194.1194.1204.1204.1204.1204.1204.1204.1204.1204.1204.1204.1204.1204.1205.1205.1205.1205.1206.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1210.1211.1211.1211.1211.1211.1211.1211.1211.1212.1212.1212.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1214.1214.1214.1214.1214.1214.1214.1214.1214.1214.1214.1214.1214.1214.1214.1214.1214.1214.1214.1214.1251.1251.1251.1251.1251.1251.1251.1423.1423.1424.1424.1424.1424.1424.1424.1424.1424.1424.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1426.1426.1426.1427.1427.1427.1427.1427.1428.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1435.1435.1435.1435.1435.1435.1435.1435.1435.1435.1439.1439.1439.1439.1439.1439.1439.1439.1439.1440.1446.1446.1446.1446.1446.1446.1451.1451.1451.1451.1451.1451.1451.1451.1642.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1645.1651.1651.1651.1651.1654.1654.1654.1654.1654.1672.1672.1672.1672.1672.1672.1672.1673.1673.1673.1673.1674.1678.1678.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1843.1843.1843.1843.1843.1843.1843.1843.2037.2037.2037.2060.2060.2060.2060.2098.2100.2100.2100.2100.2101.2102.2102.2102.2106.2106.2106.2106.2106.2106.2106.2106.2106.2106.2106.2106.2106.2295.2295.2295.2295.2295.2295.2295.2295.2295.2295.2295.2295.2304.2306.2306.2306.2306.2312.2312.2313.2314.2314.2314.2318.2318.2319.2319.2319.2319.2341.2341.2345.2345.2345.2345.2345.2345.2689.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: 19 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19.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: 94 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.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 0m23.793s user 0m22.207s sys 0m0.539s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m23.949s user 0m22.102s sys 0m0.540s Creating box around spheres Creating chemgrid maps real 0m28.025s user 0m27.458s sys 0m0.189s Atomic solvent excluded volume calculations underway FORTRAN STOP real 20m2.047s user 19m55.745s sys 0m0.268s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 518 has a net charge of 1.4000 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 518 has a net charge of 1.4000 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 518 has a net charge of 1.4000 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. 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