Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-5-37.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 FATAL got_license: could not check out a license for mmlibs version 1.9 FATAL mmerr_initialize: got_license() failed FATAL got_license: could not check out a license for mmlibs version 1.9 FATAL mmerr_initialize: got_license() failed m2io_open failed for file C.mae. sed: can't read G.ism: No such file or directory E.mol2: No such file or directory. Warning: Unable to open "ref/F2.mol2" for reading molecules. Fatal: Cannot open: ref/F2.mol2 sed: can't read H.ism: No such file or directory /bin/mv: cannot stat `ref/F2.mol2': No such file or directory ref/F.mol2: No such file or directory. ref/D.sdf: No such file or directory. ref/D.sdf: No such file or directory. FATAL mmmdl_new: could not open file ../new.sdf: No such file or directory. mmmdl_new failed. FATAL got_license: could not check out a license for mmlibs version 1.9 FATAL mmerr_initialize: got_license() failed FATAL got_license: could not check out a license for mmlibs version 1.9 FATAL mmerr_initialize: got_license() failed m2io_open failed for file C.mae. sed: can't read G.ism: No such file or directory E.mol2: No such file or directory. FATAL mmmdl_new: could not open file ../new.sdf: No such file or directory. mmmdl_new failed. FATAL got_license: could not check out a license for mmlibs version 1.9 FATAL mmerr_initialize: got_license() failed FATAL got_license: could not check out a license for mmlibs version 1.9 FATAL mmerr_initialize: got_license() failed m2io_open failed for file C.mae. sed: can't read G.ism: No such file or directory E.mol2: No such file or directory. FATAL mmmdl_new: could not open file ../new.sdf: No such file or directory. mmmdl_new failed. FATAL got_license: could not check out a license for mmlibs version 1.9 FATAL mmerr_initialize: got_license() failed FATAL got_license: could not check out a license for mmlibs version 1.9 FATAL mmerr_initialize: got_license() failed m2io_open failed for file C.mae. sed: can't read G.ism: No such file or directory E.mol2: No such file or directory. F2.mol2: No such file or directory. F2.mol2: No such file or directory. F2.mol2: No such file or directory. F2.mol2: No such file or directory. first try already in then inzinc count is 0 bzcat: Can't open input file 33: No such file or directory. bzcat: Can't open input file 70: 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 33: No such file or directory. bzcat: Can't open input file 70: 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 0m2.220s user 0m0.259s sys 0m0.355s 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 0:1344 spheres. 41. 41. 41. 41. 41. 41. 42. 42. 42. 42. 42. 46. 46. 46. 46. 46. 46. 46. 46. 46. 47. 47. 48. 48. 48. 48. 79. 79. 79. 79. 79. 80. 108. 108. 108. 108. 110. 256. 256. 256. 257. 257. 257. 257. 257. 257. 257. 257. 257. 260. 262. 263. 263. 266. 266. 273. 273. 273. 273. 273. 273. 273. 273. 273. 274. 274. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 280. 283. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 285. 286. 286. 286. 286. 286. 286. 286. 286. 286. 286. 286. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 287. 288. 288. 294. 294. 294. 294. 300. 300. 300. 300. 300. 300. 303. 303. 303. 305. 305. 305. 305. 305. 305. 305. 305. 305. 305. 305. 305. 305. 305. 305. 306. 307. 307. 307. 307. 307. 307. 307. 307. 307. 307. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 308. 310. 313. 313. 313. 313. 313. 313. 313. 313. 313. 313. 328. 328. 328. 328. 329. 329. 329. 329. 331. 331. 336. 336. 336. 336. 336. 336. 336. 336. 336. 336. 336. 336. 336. 336. 336. 336. 336. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 337. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 338. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 346. 486. 486. 486. 486. 491. 601. 601. 604. 604. 604. 609. 611. 611. 611. 611. 611. 612. 612. 612. 612. 620. 620. 620. 620. 620. 620. 620. 620. 627. 627. 627. 627. 627. 627. 627. 635. 635. 637. 637. 637. 637. 638. 638. 638. 638. 638. 638. 638. 638. 638. 638. 638. 639. 639. 641. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 656. 657. 658. 658. 658. 658. 658. 663. 665. 666. 666. 666. 666. 666. 666. 667. 667. 669. 669. 669. 669. 669. 672. 672. 672. 672. 672. 672. 672. 678. 678. 678. 678. 678. 678. 678. 678. 679. 679. 679. 679. 679. 679. 679. 679. 679. 679. 679. 679. 679. 679. 679. 680. 680. 680. 680. 680. 680. 680. 684. 684. 688. 688. 688. 688. 688. 691. 692. 692. 692. 692. 692. 692. 692. 692. 692. 692. 693. 695. 695. 695. 696. 696. 701. 701. 701. 701. 701. 701. 702. 703. 704. 704. 704. 704. 704. 709. 709. 709. 709. 709. 709. 709. 709. 709. 709. 709. 709. 709. 709. 709. 709. 710. 710. 710. 710. 711. 711. 711. 711. 711. 711. 711. 711. 711. 712. 712. 712. 712. 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. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 720. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 722. 729. 729. 729. 729. 730. 730. 730. 730. 730. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 731. 735. 735. 735. 735. 735. 735. 735. 735. 735. 735. 735. 735. 735. 736. 736. 736. 737. 737. 737. 737. 737. 737. 737. 737. 737. 737. 737. 737. 737. 737. 737. 737. 737. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 738. 739. 739. 739. 739. 739. 739. 739. 739. 739. 739. 739. 739. 739. 739. 739. 739. 739. 739. 739. 739. 741. 741. 741. 741. 741. 744. 744. 744. 744. 744. 744. 744. 747. 748. 752. 752. 752. 752. 752. 752. 752. 752. 752. 752. 752. 752. 752. 752. 752. 753. 753. 770. 770. 888. 888. 888. 889. 889. 889. 889. 889. 889. 889. 889. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 890. 903. 903. 903. 903. 903. 903. 903. 910. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 913. 913. 913. 913. 913. 913. 913. 913. 913. 913. 913. 913. 913. 913. 913. 913. 913. 913. 913. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 914. 916. 916. 916. 926. 930. 930. 930. 930. 930. 930. 930. 930. 930. 930. 930. 930. 930. 930. 930. 930. 931. 931. 931. 931. 931. 932. 932. 932. 932. 932. 932. 932. 932. 932. 932. 932. 932. 932. 932. 932. 932. 932. 932. 933. 933. 933. 933. 933. 933. 933. 933. 933. 934. 934. 934. 934. 935. 935. 935. 936. 936. 936. 936. 936. 945. 945. 945. 946. 946. 946. 946. 947. 947. 947. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 948. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 966.1023.1023.1029.1030.1030.1030.1037.1037.1037.1051.1051.1052.1052.1053.1053.1053.1053.1053.1053.1053.1053.1054.1054.1054.1054.1054.1054.1054.1054.1054.1054.1054.1062.1062.1062.1062.1062.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1063.1064.1064.1064.1064.1064.1064.1064.1115.1115.1122.1122.1123.1123.1123.1123.1123.1123.1123.1123.1123.1123.1131.1131.1132.1132.1132.1133.1133.1133.1133.1133.1133.1133.1135.1135.1135.1135.1135.1135.1135.1140.1141.1141.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1142.1143.1143.1143.1144.1144.1144.1144.1144.1144.1145.1145.1145.1145.1145.1145.1145.1145.1148.1148.1148.1148.1148.1148.1149.1187.1187.1187.1187.1187.1187.1187.1187.1187.1187.1187.1187.1187.1187.1188.1188.1194.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1195.1198.1198.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1201.1201.1201.1201.1201.1256.1256.1256.1256.1256.1256.1256.1256.1256.1256.1256.1256.1256.1256.1256.1256.1256.1259.1259.1259.1259.1259.1259.1259.1259.1263.1263.1268.1268.1268.1268.1268.1271.1271.1289.1289.1289.1289.1289.1296.1296.1297.1297.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1305.1313.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: 23 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23.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 0m33.476s user 0m30.292s sys 0m0.886s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m32.488s user 0m30.189s sys 0m0.797s Creating box around spheres Creating chemgrid maps real 0m20.966s user 0m19.637s sys 0m0.266s Atomic solvent excluded volume calculations underway FORTRAN STOP real 34m14.385s user 34m13.249s sys 0m0.275s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: LYS 224 has a net charge of -0.2720 !!! WARNING: LYS 224 has a net charge of -0.2720 !!! WARNING: LYS 224 has a net charge of -0.2720 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 42 Number of atoms in ligand - 0 IL IS 1627 NR IS- 1 INTERNAL BEGUN INTERNAL COMPLETED 18 NUMLIG IS- 18 TOTAL NUMBER OF ORIENTATIONS WRITEN IS - 0 filtering complete mf7.csh - site preparation complete, preliminary docking queued