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 0m1.759s user 0m0.307s sys 0m0.205s 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 0:1026 spheres. 63. 63. 66. 66. 66. 66. 66. 66. 66. 68. 68. 68. 68. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 73. 75. 75. 75. 84. 84. 84. 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. 87. 87. 87. 87. 87. 88. 88. 185. 185. 199. 199. 199. 199. 199. 199. 200. 200. 201. 201. 201. 201. 201. 201. 201. 201. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 210. 210. 211. 211. 211. 211. 211. 212. 212. 212. 221. 221. 221. 221. 222. 224. 230. 230. 230. 230. 230. 231. 232. 371. 371. 371. 371. 371. 371. 379. 379. 379. 379. 379. 379. 379. 379. 379. 379. 379. 380. 380. 380. 380. 380. 380. 380. 380. 381. 381. 381. 381. 384. 384. 384. 384. 384. 386. 386. 386. 386. 386. 387. 387. 387. 387. 387. 387. 387. 391. 391. 392. 392. 392. 392. 392. 392. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 400. 400. 400. 400. 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. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 412. 414. 414. 414. 414. 414. 414. 414. 414. 594. 594. 596. 596. 596. 596. 596. 596. 596. 596. 596. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 597. 599. 599. 599. 599. 599. 599. 603. 608. 608. 608. 608. 610. 610. 610. 610. 611. 611. 611. 611. 611. 611. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 613. 613. 613. 618. 618. 618. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 626. 626. 626. 626. 627. 627. 627. 627. 627. 627. 627. 628. 628. 628. 628. 628. 635. 635. 635. 635. 635. 635. 636. 636. 644. 644. 644. 644. 651. 652. 652. 652. 656. 657. 657. 658. 658. 658. 658. 658. 658. 658. 658. 659. 659. 812. 812. 812. 812. 812. 812. 812. 812. 813. 813. 814. 815. 815. 815. 815. 815. 815. 815. 815. 815. 815. 817. 818. 818. 818. 818. 818. 818. 818. 818. 818. 818. 818. 818. 818. 818. 818. 818. 818. 819. 819. 819. 821. 821. 826. 830. 830. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 834. 931. 931. 931. 931. 931. 931. 931. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 938. 947. 947. 947. 947. 947. 947. 947. 947. 947. 947. 951. 956. 957. 957. 957. 957. 957. 957. 957. 957. 958. 958. 958. 967. 967. 967. 970. 970. 971. 971. 971. 971. 976. 977. 979. 979. 979. 980. 980. 980. 980.1001.1001.1117.1117.1117.1117.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1126.1126.1126.1126.1126.1127.1127.1127.1127.1135.1137.1137.1137.1137.1137.1137.1137.1137.1138.1138.1138.1138.1138.1138.1138.1138.1140.1140.1140.1140.1140.1140.1140.1146.1146.1146.1146.1146.1146.1146.1146.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1160.1160.1160.1160.1160.1160.1340.1340.1342.1342.1342.1342.1342.1342.1342.1342.1342.1342.1343.1343.1343.1343.1343.1343.1344.1344.1344.1344.1349.1349.1349.1349.1355.1355.1356.1356.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1359.1359.1359.1359.1359.1359.1362.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1366.1366.1366.1366.1366.1366.1366.1366.1372.1372.1372.1373.1373.1373.1373.1373.1374.1374.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1389.1389.1389.1389.1389.1389.1389.1389.1389.1389.1397.1397.1397.1397.1403.1403.1403.1404.1404.1404.1404.1404.1405.1405.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1429.1429.1429.1429.1429.1429.1429.1429.1429.1429.1429.1429.1501.1502.1502.1502.1504.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1512.1513.1513.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1518.1518.1518.1518.1518.1518.1518.1518.1518.1518.1518.1518.1518.1518.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1523.1524.1524.1524.1524.1524.1524.1525.1525.1527.1527.1527.1527.1527.1533.1533.1533.1533.1533.1533.1534.1534.1534.1536.1536.1536.1536.1536.1536.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1538.1538.1538.1538.1538.1538.1538.1538.1538.1538.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: 15 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15.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 1m1.364s user 0m41.223s sys 0m1.792s Adding spheres to tarted electrostatic grid we had to cook * HD2* we had to cook * NE2* we had to cook *HNE2* we had to cook *HNE1* Creating DelPhi electrostatic grid real 1m17.929s user 0m52.451s sys 0m2.117s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 1m55.865s user 1m42.058s sys 0m0.899s Atomic solvent excluded volume calculations underway FORTRAN STOP real 29m15.146s user 29m12.816s sys 0m0.074s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASH 122 has a net charge of -0.3190 !!! WARNING: ASH 122 has a net charge of -0.3190 !!! WARNING: ASH 122 has a net charge of -0.3190 End of MakeDOCK sphere and grid generation.