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 0m1.118s user 0m0.173s sys 0m0.144s 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: 913 spheres. 68. 68. 68. 68. 68. 68. 68. 68. 68. 69. 70. 70. 70. 70. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 74. 74. 74. 74. 74. 74. 77. 77. 83. 83. 83. 83. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 171. 171. 179. 179. 179. 182. 189. 189. 189. 196. 196. 198. 198. 198. 198. 198. 198. 198. 198. 202. 202. 202. 202. 208. 208. 208. 208. 208. 208. 208. 208. 208. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 211. 211. 211. 211. 211. 211. 211. 211. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 215. 219. 219. 219. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 221. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 223. 227. 227. 227. 227. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 244. 244. 244. 244. 244. 363. 363. 366. 366. 366. 366. 366. 366. 366. 369. 369. 369. 369. 369. 369. 370. 370. 370. 371. 371. 372. 372. 372. 372. 372. 372. 372. 372. 372. 372. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 373. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 377. 377. 377. 377. 377. 379. 383. 383. 383. 383. 383. 383. 383. 383. 383. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 385. 386. 386. 386. 386. 386. 386. 386. 388. 388. 388. 388. 389. 389. 411. 599. 601. 601. 601. 601. 601. 602. 602. 602. 602. 602. 602. 602. 608. 608. 613. 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. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 618. 618. 620. 623. 623. 623. 623. 623. 623. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 624. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 631. 631. 631. 631. 631. 631. 631. 633. 633. 633. 633. 633. 633. 638. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 641. 641. 937. 937. 937. 937. 937. 937. 937. 937. 937. 937. 937. 939. 939. 939. 939. 940. 940. 940. 940. 940. 940. 940. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 954. 954. 954. 955. 955. 955. 955. 955. 955. 955. 955. 955. 966. 966. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 969. 969. 969. 969. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 973. 976. 976. 976. 978. 978. 978. 978. 978. 979. 979. 979. 979. 979. 979. 979. 979. 981. 985. 985. 985. 987. 987. 987. 987. 987. 987. 987. 987. 987. 987. 988.1002.1002.1002.1002.1121.1121.1121.1124.1127.1127.1127.1127.1128.1128.1128.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1135.1136.1136.1140.1140.1140.1140.1140.1140.1141.1141.1141.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1146.1146.1146.1146.1146.1147.1147.1149.1149.1149.1149.1149.1155.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1372.1372.1372.1373.1373.1374.1374.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1378.1381.1381.1381.1381.1381.1381.1381.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1396.1396.1396.1397.1397.1397.1397.1397.1397.1398.1398.1399.1414.1414.1414.1414.1421.1421.1421.1421.1421.1421.1421.1421.1421.1422.1422.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: 14 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14.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 0m26.558s user 0m24.563s sys 0m0.643s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m41.797s user 0m29.646s sys 0m1.360s Creating box around spheres Creating chemgrid maps real 0m16.971s user 0m9.674s sys 0m0.511s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m48.725s user 18m46.506s sys 0m0.090s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.