Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-04.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 28: No such file or directory. bzcat: Can't open input file 45: 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 28: No such file or directory. bzcat: Can't open input file 45: 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 0m1.741s user 0m0.311s sys 0m0.103s 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 0:1518 spheres. 733. 733. 733. 733. 737. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 741. 743. 743. 744. 744. 744. 744. 744. 744. 744. 744. 745. 745. 745. 745. 745. 746. 746. 746. 746. 746. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 747. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 908. 908. 908. 908. 908. 908. 908. 908. 908. 908. 908. 908. 908. 909. 909. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 972. 972. 972. 972. 973. 973. 973. 981. 981. 981. 981. 981. 982. 982. 984. 984. 984. 984. 984. 984. 984. 984. 984. 984. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 986. 986. 986. 986. 986. 986. 986. 986. 987. 987. 987. 987. 987. 987. 987. 987. 987. 987. 987. 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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: 18 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18.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 had to cook * ND2* Creating DelPhi electrostatic grid real 0m23.312s user 0m21.627s sys 0m0.577s Adding spheres to tarted electrostatic grid we had to cook * ND2* Creating DelPhi electrostatic grid real 0m23.743s user 0m21.578s sys 0m0.582s Creating box around spheres we had to cook * OD1* we had to cook * ND2* Creating chemgrid maps real 0m25.727s user 0m16.825s sys 0m0.203s Atomic solvent excluded volume calculations underway FORTRAN STOP real 26m12.135s user 26m7.954s sys 0m0.037s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: HIY 389 has a net charge of 0.2000 !!! WARNING: HIZ 405 has a net charge of 0.2000 !!! WARNING: HIZ 409 has a net charge of 0.2000 !!! WARNING: HIZ 415 has a net charge of 0.2000 !!! WARNING: ZN7 749 has a net charge of 1.4000 !!! WARNING: ZN7 750 has a net charge of 1.4000 !!! WARNING: HIY 389 has a net charge of 0.2000 !!! WARNING: HIZ 405 has a net charge of 0.2000 !!! WARNING: HIZ 409 has a net charge of 0.2000 !!! WARNING: HIZ 415 has a net charge of 0.2000 !!! WARNING: ZN7 749 has a net charge of 1.4000 !!! WARNING: ZN7 750 has a net charge of 1.4000 !!! WARNING: HIY 389 has a net charge of 0.2000 !!! WARNING: HIZ 405 has a net charge of 0.2000 !!! WARNING: HIZ 409 has a net charge of 0.2000 !!! WARNING: HIZ 415 has a net charge of 0.2000 !!! WARNING: ZN7 749 has a net charge of 1.4000 !!! WARNING: ZN7 750 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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