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 0m2.285s user 0m0.457s sys 0m0.328s 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 0:1545 spheres. 67. 69. 69. 69. 71. 71. 72. 72. 72. 72. 72. 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. 75. 75. 75. 75. 76. 84. 84. 84. 85. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 172. 172. 172. 183. 183. 183. 183. 183. 183. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 197. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 219. 219. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 222. 222. 222. 222. 222. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 228. 228. 228. 228. 228. 228. 228. 228. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 231. 244. 255. 258. 258. 258. 258. 258. 258. 261. 261. 262. 348. 348. 353. 353. 353. 353. 353. 353. 353. 353. 353. 354. 354. 354. 354. 354. 354. 358. 358. 359. 359. 362. 362. 362. 362. 362. 362. 364. 367. 367. 367. 370. 370. 370. 371. 373. 373. 373. 373. 373. 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. 374. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 377. 377. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 379. 384. 384. 384. 384. 384. 384. 384. 384. 387. 387. 388. 388. 389. 389. 389. 390. 390. 390. 392. 392. 392. 392. 392. 392. 392. 392. 392. 398. 398. 398. 398. 398. 398. 400. 401. 401. 401. 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. 404. 404. 404. 404. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 407. 410. 411. 411. 411. 411. 411. 411. 411. 412. 412. 583. 583. 583. 583. 583. 583. 583. 583. 583. 583. 583. 585. 585. 585. 585. 585. 585. 585. 585. 585. 585. 585. 585. 585. 585. 585. 594. 594. 595. 598. 598. 598. 598. 598. 598. 598. 598. 598. 598. 598. 598. 598. 598. 600. 600. 600. 600. 600. 601. 601. 601. 601. 601. 602. 602. 602. 609. 612. 614. 614. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 615. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 617. 617. 617. 617. 617. 617. 617. 619. 622. 622. 622. 622. 622. 622. 623. 623. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 632. 639. 639. 639. 639. 639. 640. 640. 640. 640. 640. 655. 655. 660. 661. 661. 661. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 663. 663. 663. 665. 665. 665. 665. 665. 665. 667. 668. 668. 668. 668. 668. 668. 668. 668. 669. 669. 669. 671. 671. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 821. 821. 821. 821. 821. 821. 821. 821. 821. 821. 823. 823. 824. 824. 824. 824. 824. 824. 824. 824. 825. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 826. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 830. 830. 830. 830. 831. 838. 839. 839. 839. 840. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 842. 843. 843. 843. 843. 843. 843. 843. 843. 927. 937. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 945. 954. 954. 954. 954. 954. 954. 954. 954. 954. 954. 954. 964. 964. 964. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 967. 967. 967. 967. 967. 967. 967. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 971. 974. 975. 976. 976. 976. 976. 976. 976. 976. 976. 976. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 983. 983. 983. 983. 983. 983. 984. 984. 984. 984. 984. 984. 984. 984. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 985. 986. 986. 986. 987. 999. 999. 999. 999.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1000.1101.1101.1101.1103.1103.1103.1103.1103.1104.1107.1107.1107.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1112.1113.1113.1113.1113.1114.1114.1114.1114.1115.1117.1117.1117.1117.1117.1117.1119.1120.1122.1122.1122.1122.1122.1122.1122.1122.1124.1124.1125.1125.1125.1125.1126.1126.1126.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1133.1133.1134.1135.1135.1137.1137.1137.1137.1137.1137.1138.1138.1138.1138.1138.1138.1138.1138.1140.1141.1141.1141.1141.1141.1141.1144.1145.1145.1145.1145.1145.1145.1145.1145.1147.1147.1147.1147.1147.1147.1147.1147.1147.1153.1153.1153.1153.1153.1153.1153.1153.1153.1155.1156.1157.1157.1157.1157.1157.1157.1157.1157.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1158.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1162.1166.1166.1171.1171.1171.1171.1171.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1172.1173.1173.1173.1173.1173.1173.1174.1174.1174.1174.1175.1176.1176.1176.1176.1178.1179.1179.1179.1179.1179.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1182.1182.1338.1338.1338.1338.1338.1338.1338.1340.1340.1340.1340.1340.1340.1340.1349.1349.1349.1350.1350.1354.1355.1355.1355.1355.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1356.1357.1357.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1358.1361.1362.1362.1362.1363.1364.1364.1364.1368.1368.1369.1369.1369.1369.1369.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1374.1377.1377.1377.1378.1378.1378.1378.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1385.1385.1385.1385.1385.1387.1387.1387.1387.1387.1387.1387.1387.1387.1394.1394.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1410.1416.1416.1416.1417.1417.1417.1417.1417.1417.1417.1417.1417.1417.1418.1418.1418.1420.1420.1420.1420.1423.1423.1423.1423.1423.1423.1423.1424.1424.1424.1424.1424.1424.1426.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: 49 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. 46. 47. 48. 49.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 we had to cook * HD2* Creating DelPhi electrostatic grid real 0m48.761s user 0m28.511s sys 0m0.883s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 0m52.703s user 0m28.566s sys 0m0.876s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 0m42.127s user 0m41.189s sys 0m0.319s Atomic solvent excluded volume calculations underway FORTRAN STOP real 31m54.525s user 31m53.938s sys 0m0.167s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASH 125 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 End of MakeDOCK sphere and grid generation.