MakeDOCK 2.0, modified by J.J.Irwin and M.Mysinger, Feb 2008. Original version by D.M.Lorber, Oct 2000. Contributions from B.Q.Wei, A.N.Kirschner, and N.Huang Using scripts in /raid1/soft/dock67. Creating binding-site residue list Creating molecular surface 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 0:2058 spheres. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 414. 414. 414. 414. 429. 429. 429. 430. 430. 430. 430. 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. 432. 432. 434. 434. 434. 452. 452. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 455. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 458. 458. 458. 460. 460. 460. 462. 462. 462. 462. 462. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 463. 550. 553. 556. 557. 557. 557. 557. 557. 557. 557. 562. 562. 562. 562. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 563. 569. 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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: 21 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 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. 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. 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. Coloring matching spheres Creating box around spheres Creating distmap shape-complementarity grid Adding spheres to electrostatic grid Creating DelPhi electrostatic grid Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid Creating chemgrid maps Creating solvmap occluded volume desolvation grid Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.