Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-1-40.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 01: No such file or directory. bzcat: Can't open input file 74: 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 01: No such file or directory. bzcat: Can't open input file 74: 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 0m3.855s user 0m0.626s sys 0m0.517s 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: 926 spheres. 170. 170. 170. 170. 170. 171. 171. 172. 172. 172. 172. 172. 172. 172. 180. 180. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 186. 187. 187. 187. 189. 189. 189. 189. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 192. 192. 192. 192. 192. 192. 192. 192. 192. 192. 196. 196. 196. 196. 196. 196. 196. 196. 204. 204. 204. 207. 209. 291. 291. 291. 291. 291. 291. 291. 291. 291. 291. 291. 291. 298. 298. 310. 310. 314. 402. 404. 404. 404. 404. 404. 404. 404. 405. 405. 405. 405. 408. 408. 409. 409. 409. 409. 409. 409. 409. 409. 409. 409. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 414. 414. 414. 414. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 416. 416. 416. 416. 416. 416. 418. 418. 418. 420. 421. 424. 424. 424. 424. 424. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 425. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 432. 432. 432. 432. 432. 432. 432. 432. 432. 432. 432. 432. 432. 432. 432. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 433. 434. 436. 437. 437. 438. 438. 438. 438. 438. 439. 442. 442. 442. 442. 442. 442. 442. 442. 442. 443. 443. 443. 443. 443. 443. 443. 443. 443. 443. 444. 444. 444. 444. 444. 444. 444. 444. 444. 444. 444. 444. 444. 444. 446. 446. 446. 446. 446. 446. 446. 446. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 448. 448. 448. 448. 448. 448. 448. 448. 448. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 479. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 656. 656. 658. 787. 787. 787. 787. 787. 787. 789. 790. 790. 790. 790. 790. 790. 790. 790. 790. 790. 792. 792. 792. 792. 792. 792. 792. 792. 792. 792. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 793. 794. 794. 794. 794. 794. 794. 794. 804. 806. 806. 806. 806. 806. 807. 807. 807. 807. 807. 807. 807. 808. 808. 808. 808. 809. 809. 809. 809. 809. 809. 828. 828. 828. 828. 829. 829. 829. 996. 997. 997. 997. 997. 997.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1006.1019.1019.1019.1021.1021.1021.1021.1021.1021.1021.1021.1021.1021.1021.1021.1021.1021.1021.1021.1022.1023.1023.1023.1023.1023.1024.1024.1041.1041.1041.1041.1041.1041.1041.1045.1047.1048.1048.1048.1048.1048.1048.1050.1050.1052.1055.1055.1055.1055.1055.1055.1055.1055.1055.1055.1055.1055.1055.1055.1154.1164.1164.1164.1168.1168.1168.1168.1169.1169.1169.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1173.1175.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1178.1179.1404.1404.1404.1404.1404.1404.1405.1405.1405.1405.1405.1405.1405.1405.1405.1413.1413.1413.1414.1414.1415.1419.1419.1419.1424.1424.1424.1424.1424.1424.1424.1424.1424.1424.1424.1424.1424.1516.1516.1516.1516.1516.1516.1516.1516.1516.1516.1516.1516.1516.1516.1516.1521.1521.1528.1528.1529.1529.1529.1529.1530.1530.1530.1530.1534.1534.1534.1534.1534.1534.1534.1534.1546.1546.1546.1549.1549.1549.1549.1549.1549.1788.1788.1788.1788.1788.1788.1788.1788.1788.1788.1788.1788.1790.1790.1790.1793.1793.1793.1793.1794.1794.1794.1794.1796.1796.1796.1796.1796.1796.1796.1796.1797.1797.1797.1797.1942.1942.1942.1942.1942.1942.1942.1942.1942.1942.1942.1942.1942.1942.1942.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1944.1948.1955.1955.1955.1955.1956.1958.1960.1960.1962.1962.1962.1962.1962.1962.1964.1964.1964.1964.1964.2138.2138.2138.2138.2138.2138.2138.2138.2138.2138.2138.2139.2139.2139.2139.2139.2141.2141.2141.2141.2142.2142.2142.2142.2142.2142.2142.2143.2143.2143.2143.2143.2143.2143.2143.2343.2343.2343.2343.2343.2343.2343.2348.2348.2348.2348.2348.2352.2352.2352.2353.2353.2353.2353.2358.2358.2361.2364.2365.2365.2365.2365.2365.2365.2365.2365.2365.2365.2365.2365.2365.2365.2365.2365.2492.2492.2492.2492.2492.2492.2492.2492.2509.2509.2509.2510.2510.2510.2510.2510.2510.2510.2513.2513.2564.2564.2566.2566.2566.2566.2566.2566.2566.2566.2567.2567.2568.2568.2569.2569.2569.2569.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 1m19.624s user 0m31.536s sys 0m1.029s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m42.324s user 0m38.200s sys 0m1.600s Creating box around spheres Creating chemgrid maps real 1m27.786s user 1m26.588s sys 0m0.561s Atomic solvent excluded volume calculations underway FORTRAN STOP real 27m46.556s user 27m45.618s sys 0m0.242s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar failed to get similars