Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-28.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 25: No such file or directory. bzcat: Can't open input file 01: 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 25: No such file or directory. bzcat: Can't open input file 01: 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 0m10.853s user 0m0.267s sys 0m0.151s 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: 932 spheres. 666. 666. 666. 666. 666. 666. 666. 666. 666. 666. 667. 667. 667. 667. 667. 667. 670. 702. 705. 705. 705. 705. 705. 705. 705. 706. 706. 706. 706. 706. 706. 706. 707. 707. 707. 707. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 708. 709. 709. 710. 710. 710. 710. 710. 710. 710. 710. 710. 710. 710. 710. 710. 711. 711. 711. 711. 711. 711. 711. 711. 712. 712. 712. 712. 712. 712. 712. 712. 712. 712. 714. 714. 714. 714. 714. 719. 719. 719. 719. 719. 720. 720. 720. 720. 720. 720. 725. 725. 731. 737. 737. 737. 737. 738. 738. 738. 738. 759. 760. 760. 760. 760. 761. 762. 762. 762. 762. 764. 764. 764. 764. 764. 764. 764. 764. 765. 766. 766. 766. 766. 766. 766. 766. 766. 767. 767. 767. 773. 773. 773. 773. 773. 773. 773. 773. 773. 773. 773. 773. 773. 773. 773. 773. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 774. 775. 775. 775. 775. 775. 775. 775. 775. 775. 775. 775. 775. 775. 775. 781. 782. 782. 783. 783. 783. 783. 783. 783. 783. 783. 783. 783. 783. 783. 783. 783. 784. 785. 785. 789. 789. 789. 789. 789. 789. 789. 789. 789. 789. 791. 793. 793. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 796. 799. 799. 803. 803. 803. 803. 803. 803. 806. 807. 807. 807. 807. 807. 807. 807. 807. 807. 807. 807. 807. 807. 807. 807. 807. 807. 807. 807. 807. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 817. 819. 819. 819. 819. 902. 902. 902. 902. 902. 902. 902. 902. 906. 906. 906. 906. 906. 906. 906. 906. 909. 909. 909. 950. 971.1044.1044.1044.1044.1044.1046.1046.1046.1046.1046.1046.1046.1046.1046.1046.1046.1048.1048.1048.1048.1048.1048.1058.1058.1058.1058.1058.1058.1058.1058.1058.1058.1058.1058.1058.1058.1058.1058.1073.1073.1073.1073.1073.1076.1076.1076.1076.1076.1076.1076.1076.1076.1078.1080.1080.1080.1080.1080.1080.1080.1080.1080.1080.1080.1080.1080.1080.1083.1083.1085.1085.1085.1085.1085.1085.1085.1086.1088.1088.1088.1088.1088.1091.1095.1095.1095.1095.1095.1095.1095.1095.1096.1114.1114.1114.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1117.1118.1119.1119.1130.1130.1130.1154.1156.1156.1156.1157.1197.1197.1198.1199.1199.1199.1199.1199.1204.1204.1204.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1209.1212.1212.1212.1212.1212.1241.1241.1241.1242.1242.1242.1246.1246.1246.1247.1247.1251.1251.1251.1251.1251.1251.1251.1251.1251.1251.1252.1252.1252.1252.1252.1252.1253.1253.1253.1253.1253.1257.1258.1258.1258.1258.1258.1262.1262.1262.1262.1262.1262.1262.1264.1264.1267.1267.1267.1267.1267.1267.1267.1267.1267.1267.1267.1267.1267.1283.1287.1288.1289.1292.1292.1293.1293.1293.1293.1293.1293.1293.1293.1293.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1294.1295.1295.1295.1296.1296.1296.1296.1296.1296.1296.1296.1296.1296.1300.1300.1300.1301.1301.1301.1301.1301.1301.1303.1303.1303.1303.1303.1303.1303.1303.1304.1304.1304.1304.1304.1304.1304.1304.1304.1304.1304.1304.1304.1304.1304.1304.1304.1304.1305.1305.1305.1305.1305.1305.1308.1308.1308.1308.1308.1310.1311.1311.1311.1313.1313.1313.1316.1316.1318.1318.1319.1319.1319.1319.1319.1319.1324.1324.1324.1324.1324.1324.1324.1324.1324.1324.1324.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1326.1326.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1327.1328.1328.1328.1329.1329.1329.1329.1329.1341.1341.1341.1341.1346.1346.1346.1346.1346.1346.1346.1346.1346.1346.1346.1346.1347.1348.1348.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1350.1350.1351.1351.1351.1354.1355.1355.1355.1355.1355.1358.1358.1358.1358.1358.1358.1358.1358.1358.1359.1359.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1365.1366.1366.1366.1366.1367.1371.1372.1376.1378.1378.1378.1381.1381.1381.1381.1381.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1383.1561.1566.1566.1566.1566.1566.1566.1566.1566.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1568.1570.1570.1570.1570.1570.1570.1570.1570.1570.1846.1846.1846.1846.1846.1846.1846.1846.1846.1846.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: 28 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.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 0m29.501s user 0m27.407s sys 0m0.861s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m29.613s user 0m27.593s sys 0m0.838s Creating box around spheres Creating chemgrid maps real 0m10.815s user 0m10.242s sys 0m0.301s Atomic solvent excluded volume calculations underway FORTRAN STOP real 26m53.595s user 19m2.875s sys 0m0.437s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HIZ 233 has a net charge of 0.2000 !!! WARNING: HIZ 248 has a net charge of 0.2000 !!! WARNING: HIY 261 has a net charge of 0.2000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 has a net charge of 1.4000 !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HIZ 233 has a net charge of 0.2000 !!! WARNING: HIZ 248 has a net charge of 0.2000 !!! WARNING: HIY 261 has a net charge of 0.2000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 has a net charge of 1.4000 !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HIZ 233 has a net charge of 0.2000 !!! WARNING: HIZ 248 has a net charge of 0.2000 !!! WARNING: HIY 261 has a net charge of 0.2000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 has a net charge of 1.4000 End of MakeDOCK sphere and grid generation. Grid preparation completed normally. going into second inactives test after second inactives finished ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory Permission denied, please try again. ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory Permission denied, please try again. ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory Permission denied (publickey,gssapi-with-mic,password). FILTER PROGRAM THIS PROGRAM FILTERS ATOMIC COORDINATE FILES BASED ON DISTANCE AND SEQUENCE CRITERIA name of file to filter by - xtal-lig.pdb filter by atom names or numbers in receptor(na/nu)? residue/ligand orientation number increment filter? -100000 Filter for MS run?(Y/N) N Either names or numbers of the atoms to filter by, as they appear in the pdb, with boolean and/or operators if such apply between them. Maximum of one boolean per two filter atoms. name of ligand file- rec.pdb names of ligand atoms to match against receptor filters. Include boolean and/ors between EACH atom specified. LIGAND ATOM 1ISALL internal filtering? Y distance cutoffs for each of the receptor atoms specified- 25.00000 output filename- poc.txt number of allowed ligand contacts in an all-filter? LIGBUM IS- 0 IR IS 48 Number of atoms in ligand - 0 IL IS 1848 NR IS- 1 INTERNAL BEGUN INTERNAL COMPLETED 22 NUMLIG IS- 22 TOTAL NUMBER OF ORIENTATIONS WRITEN IS - 0 filtering complete mf7.csh - site preparation complete, preliminary docking queued