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 0m1.144s user 0m0.209s sys 0m0.127s 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 0:1325 spheres. 68. 68. 68. 68. 68. 69. 69. 70. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 72. 72. 72. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 75. 76. 76. 76. 76. 84. 84. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 182. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 197. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 219. 219. 219. 219. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 221. 222. 222. 223. 223. 223. 223. 223. 223. 228. 228. 228. 228. 228. 228. 229. 229. 229. 229. 229. 229. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 245. 347. 347. 347. 347. 348. 348. 348. 348. 348. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 354. 354. 354. 354. 358. 358. 358. 358. 361. 361. 361. 361. 362. 362. 362. 362. 362. 362. 362. 367. 367. 367. 367. 367. 367. 367. 367. 367. 367. 369. 369. 369. 370. 370. 370. 370. 373. 373. 373. 373. 373. 373. 373. 373. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 374. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 378. 378. 379. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 385. 388. 388. 389. 389. 389. 389. 389. 389. 390. 390. 390. 390. 390. 392. 392. 392. 392. 392. 392. 392. 392. 392. 397. 397. 397. 398. 398. 398. 398. 398. 398. 398. 399. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 403. 404. 404. 404. 404. 404. 404. 404. 404. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 407. 407. 412. 412. 412. 414. 414. 417. 418. 418. 418. 418. 419. 419. 420. 422. 422. 422. 422. 422. 422. 422. 422. 424. 424. 585. 585. 585. 585. 585. 585. 587. 587. 587. 587. 587. 587. 600. 600. 602. 602. 602. 603. 603. 603. 603. 604. 604. 604. 604. 605. 605. 605. 605. 605. 605. 605. 609. 609. 609. 609. 611. 616. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 618. 619. 619. 621. 624. 625. 625. 625. 625. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 634. 634. 634. 634. 634. 640. 641. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 657. 657. 657. 657. 657. 657. 663. 663. 663. 663. 664. 664. 664. 664. 664. 664. 664. 664. 664. 665. 665. 665. 665. 665. 665. 667. 667. 667. 667. 668. 670. 670. 670. 670. 670. 670. 670. 671. 671. 671. 671. 671. 671. 671. 671. 671. 823. 823. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 828. 828. 828. 828. 828. 828. 828. 828. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 832. 841. 841. 841. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 929. 940. 940. 940. 940. 940. 940. 940. 940. 954. 954. 954. 954. 954. 955. 956. 956. 956. 956. 956. 956. 956. 960. 965. 966. 966. 966. 966. 966. 966. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 969. 969. 969. 969. 969. 969. 969. 969. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 973. 976. 977. 977. 978. 978. 978. 978. 978. 979. 979. 979. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 981. 985. 985. 985. 985. 987. 987. 987. 987. 987. 987. 987. 988. 988. 988. 988. 988. 988. 989.1002.1002.1002.1002.1002.1002.1002.1002.1002.1002.1002.1012.1012.1012.1012.1012.1012.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1015.1015.1015.1015.1015.1015.1015.1015.1015.1015.1017.1018.1018.1018.1019.1019.1019.1019.1110.1110.1110.1110.1110.1110.1110.1110.1110.1111.1115.1115.1115.1116.1118.1119.1119.1119.1121.1121.1124.1124.1124.1124.1124.1124.1124.1124.1127.1127.1127.1127.1128.1128.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1135.1135.1139.1139.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1141.1141.1141.1142.1142.1142.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1146.1146.1146.1147.1147.1147.1147.1147.1149.1149.1149.1149.1149.1149.1149.1149.1149.1154.1154.1155.1155.1155.1155.1155.1158.1158.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1169.1169.1181.1181.1181.1357.1357.1357.1357.1357.1357.1359.1359.1360.1360.1360.1360.1360.1360.1360.1360.1362.1366.1371.1371.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1381.1381.1381.1381.1381.1381.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1383.1383.1383.1383.1391.1391.1391.1391.1391.1391.1391.1391.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1414.1414.1414.1414.1420.1420.1420.1421.1421.1421.1421.1421.1421.1421.1421.1421.1422.1424.1424.1424.1424.1424.1427.1427.1427.1427.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.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: 45 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. 33. 34. 35. 36. 37. 38. 39. 40. 41. 42. 43. 44. 45.FORTRAN STOP Adding essential hydrogens to receptor Adding all-atom hydrogens... Working on structure 1 Pre-treating metals... Done treating metals Adding hydrogens... Treating metals... Creating di-sulfur bonds... Finding het groups... Coloring atoms by element (green carbons in hets)... Running ProtAssign... using exhaustive mode will sample waters done with preparation Writing to file... DONE. Output file: rec.mae Removing non-polar hydrogens... Renaming polar hydrogens... 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 0m37.032s user 0m28.665s sys 0m1.366s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m24.385s user 0m31.674s sys 0m1.044s Creating box around spheres Creating chemgrid maps real 0m13.672s user 0m11.586s sys 0m0.565s Atomic solvent excluded volume calculations underway FORTRAN STOP real 16m48.123s user 16m47.670s sys 0m0.115s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.