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 0m36.969s user 0m0.565s sys 0m0.337s 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 0:1692 spheres. 398. 398. 398. 398. 398. 398. 398. 398. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 402. 402. 402. 405. 405. 405. 405. 405. 405. 405. 405. 407. 408. 408. 408. 408. 408. 408. 408. 408. 409. 409. 409. 409. 409. 409. 409. 409. 409. 409. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 438. 442. 442. 442. 443. 443. 443. 443. 443. 443. 443. 443. 444. 444. 444. 444. 444. 444. 444. 445. 445. 445. 445. 445. 600. 605. 605. 605. 605. 605. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 606. 614. 614. 614. 614. 614. 614. 614. 620. 621. 622. 622. 622. 622. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 629. 629. 629. 630. 630. 630. 630. 630. 631. 631. 631. 631. 631. 631. 631. 631. 631. 631. 632. 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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: 22 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22.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... Created a bond between residue(A:15) and residue(A:4); changed residue names to "CYX " Created a bond between residue(A:25) and residue(A:9); changed residue names to "CYX " Created a bond between residue(A:37) and residue(A:27); changed residue names to "CYX " Created a bond between residue(A:128) and residue(A:5); changed residue names to "CYX " Created a bond between residue(A:544) and residue(A:538); changed residue names to "CYX " Created a bond between residue(B:567) and residue(B:556); changed residue names to "CYX " Created a bond between residue(B:577) and residue(B:561); changed residue names to "CYX " Created a bond between residue(B:589) and residue(B:579); changed residue names to "CYX " 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 1m26.638s user 0m27.472s sys 0m0.712s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m12.389s user 0m26.718s sys 0m0.702s Creating box around spheres Creating chemgrid maps real 0m41.311s user 0m17.108s sys 0m0.239s Atomic solvent excluded volume calculations underway FORTRAN STOP real 43m10.226s user 15m51.492s sys 0m0.103s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.