Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-12.c.bkslab.org du2 starts 1 molecule processed, 0 errors convert.py (MDL SDF -> Isomeric SMILES): mols in: 2 mols out: 2 Total: 2 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 91: No such file or directory. bzcat: Can't open input file 34: 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 91: No such file or directory. bzcat: Can't open input file 34: 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 0m2.123s user 0m0.297s sys 0m0.271s 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 0:1430 spheres. 166. 166. 166. 166. 166. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 176. 177. 177. 177. 178. 178. 178. 179. 179. 179. 179. 179. 179. 179. 179. 179. 179. 179. 179. 179. 179. 179. 179. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 181. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 185. 188. 188. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 200. 200. 200. 200. 200. 201. 201. 201. 201. 201. 201. 201. 201. 201. 201. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 211. 388. 388. 388. 388. 388. 388. 389. 389. 389. 389. 389. 389. 389. 389. 389. 389. 389. 389. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 390. 392. 392. 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441. 441. 441. 441. 441. 441. 441. 441. 441. 442. 442. 442. 442. 443. 443. 443. 443. 443. 444. 462. 462. 462. 462. 462. 462. 462. 462. 462. 462. 462. 462. 462. 462. 462. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 486. 486. 486. 486. 488. 488. 489. 489. 502. 502. 510. 510. 510. 510. 510. 510. 510. 510. 510. 510. 510. 510. 589. 589. 593. 594. 594. 594. 594. 594. 594. 594. 618. 618. 618. 618. 618. 618. 618. 618. 620. 620. 620. 620. 620. 620. 620. 620. 628. 628. 631. 631. 631. 632. 632. 633. 634. 634. 634. 634. 634. 634. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 635. 636. 636. 636. 636. 636. 636. 636. 636. 638. 638. 638. 638. 638. 638. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 640. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 649. 649. 649. 651. 652. 652. 652. 652. 652. 652. 652. 653. 653. 654. 654. 654. 654. 654. 654. 654. 654. 654. 654. 656. 656. 656. 656. 656. 656. 656. 656. 658. 658. 663. 665. 665. 665. 667. 667. 669. 669. 669. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 677. 677. 677. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 679. 679. 679. 679. 679. 679. 715. 715. 715. 715. 715. 715. 715. 715. 715. 715. 715. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 717. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 719. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 852. 854. 854. 854. 854. 854. 854.1240.1244.1244.1244.1244.1244.1244.1245.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1246.1249.1249.1249.1249.1249.1249.1249.1249.1249.1249.1249.1249.1249.1249.1249.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1250.1255.1255.1255.1256.1256.1256.1256.1256.1257.1257.1257.1257.1274.1274.1274.1274.1274.1274.1274.1274.1274.1274.1274.1274.1274.1274.1274.1274.1274.1274.1274.1274.1278.1415.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1428.1428.1428.1428.1428.1428.1428.1429.1430.1430.1430.1436.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1438.1440.1440.1440.1440.1440.1440.1440.1440.1440.1454.1461.1462.1462.1462.1463.1463.1463.1463.1463.1464.1464.1464.1464.1464.1466.1466.1466.1475.1475.1475.1504.1504.1505.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1705.1705.1705.1706.1706.1707.1707.1707.1708.1709.1709.1709.1709.1709.1710.1710.1710.1711.1711.1716.1716.1716.1716.1716.1716.1718.1720.1723.1723.1724.1724.1724.1724.1724.1725.1725.1727.1727.1732.1733.1733.1733.1733.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1734.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1737.1737.1737.1737.1737.1737.1737.1737.2055.2055.2055.2055.2055.2055.2057.2057.2057.2057.2057.2057.2061.2061.2061.2061.2061.2061.2061.2061.2061.2061.2061.2061.2061.2061.2061.2061.2098.2098.2098.2098.2098.2098.2098.2098.2099.2099.2099.2099.2099.2099.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2100.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2101.2102.2102.2102.2102.2102.2102.2102.2104.2104.2104.2296.2296.2296.2296.2302.2302.2302.2302.2302.2302.2302.2302.2302.2302.2305.2305.2305.2310.2310.2310.2310.2311.2311.2311.2311.2313.2313.2313.2313.2313.2315.2315.2315.2316.2316.2316.2316.2316.2316.2316.2316.2316.2316.2316.2317.2317.2663.2663.2663.2663.2663.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2664.2665.2665.2665.2665.2665.2665.2665.2665.2665.2665.2665.2665.2665.2665.2665.2667.2667.2668.2668.2668.2668.2668.2668.2671.2671.2673.2674.2674.2674.2674.2674.2676.2678.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: 32 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.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 * OP2* we had to cook * OP1* Creating DelPhi electrostatic grid real 0m26.072s user 0m24.274s sys 0m0.625s Adding spheres to tarted electrostatic grid we had to cook * OP2* we had to cook * OP1* Creating DelPhi electrostatic grid real 0m26.504s user 0m24.157s sys 0m0.610s Creating box around spheres we had to cook * OP2* we had to cook * OP1* Creating chemgrid maps real 0m12.251s user 0m11.582s sys 0m0.218s Atomic solvent excluded volume calculations underway FORTRAN STOP real 15m34.413s user 15m33.905s sys 0m0.084s Checking for WARNINGS in OUTPARM. WARNING--parameters not found for ATOM 3315 OP3 UMP 557 sqrt(A), sqrt(B), and charge set to 0.0 Checking for WARNINGS in delphi.log. !!! WARNING: UMP 557 has a net charge of -0.1000 !!! WARNING: UMP 557 has a net charge of -0.1000 !!! WARNING: UMP 557 has a net charge of -0.1000 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 52 Number of atoms in ligand - 0 IL IS 2679 NR IS- 1 INTERNAL BEGUN INTERNAL COMPLETED 20 NUMLIG IS- 20 TOTAL NUMBER OF ORIENTATIONS WRITEN IS - 1 filtering complete mf7.csh - site preparation complete, preliminary docking queued